[REVIEW]: serp: An R package for smoothing in ordinal regression #3705

whedon · 2021-09-09T14:08:08Z

Submitting author: @ejikeugba (Ejike Ugba)
Repository: https://github.com/ejikeugba/serp
Version: v0.2.2
Editor: @Bisaloo
Reviewer: @bernardsilenou, @wesleyburr
Archive: 10.5281/zenodo.5596864

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Review checklist for @bernardsilenou

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Documentation

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Software paper

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Review checklist for @wesleyburr

✨ 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. ✨

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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 (@ejikeugba) 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 · 2021-09-09T14:08:12Z

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

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

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whedon · 2021-09-09T14:08:18Z

Wordcount for paper.md is 1543

whedon · 2021-09-09T14:08:19Z

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.03 s (955.2 files/s, 131750.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               15            127            664           1838
Markdown                         4             92              0            258
TeX                              1             27              0            220
YAML                             5             45              9            201
Rmd                              1             26             72              7
-------------------------------------------------------------------------------
SUM:                            26            317            745           2524
-------------------------------------------------------------------------------


Statistical information for the repository 'edb7629ff7ea7e2f21e78c6c' was
gathered on 2021/09/09.
No commited files with the specified extensions were found.

whedon · 2021-09-09T14:08:26Z

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

OK DOIs

- 10.1002/9780470594001 is OK
- doi.org/10.4137/CIN.S20806 is OK
- 10.1080/00401706.2000.10485983 is OK
- 10.1002/wics.1296 is OK
- 10.2307/2347760 is OK
- 10.1177/1471082X16642560 is OK
- 10.3390/stats4030037 is OK
- 10.1080/01621459.2016.1180986 is OK
- 10.1111/j.1467-9868.2005.00503.x is OK

MISSING DOIs

- 10.2307/2288515 may be a valid DOI for title: Advanced Econometrics: A Bridge to the Literature
- 10.1007/bf02985802 may be a valid DOI for title: The Elements of Statistical Learning: Data Mining, Inference and Prediction
- 10.18637/jss.v099.i06 may be a valid DOI for title: Regularized ordinal regression and the ordinalNet R package

INVALID DOIs

- None

whedon · 2021-09-09T14:08:36Z

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

Bisaloo · 2021-09-20T07:39:09Z

👋👋 @bernardsilenou @wesleyburr, as agreed this is a friendly reminder about your review for the serp R package and the associated paper.

This is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread with the JOSS requirements. 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 and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#3705 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@Bisaloo) if you have any questions/concerns.

Bisaloo · 2021-09-22T08:16:39Z

@whedon re-invite @bernardsilenou as reviewer

whedon · 2021-09-22T08:16:44Z

OK, the reviewer has been re-invited.

@bernardsilenou please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

bernardsilenou · 2021-09-22T12:39:31Z

Done! Thanks, Bernard

…

________________________________ From: Hugo Gruson ***@***.***> Sent: 22 September 2021 10:16:49 To: openjournals/joss-reviews Cc: Silenou, Bernard; Mention Subject: Re: [openjournals/joss-reviews] [REVIEW]: serp: An R package for smoothing in ordinal regression (#3705) @whedon<https://github.com/whedon> re-invite @bernardsilenou<https://github.com/bernardsilenou> as reviewer — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3705 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ADDFA5D3UI7VLDYUCCPBFY3UDGGHDANCNFSM5DXHJUFQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

whedon · 2021-09-23T14:08:17Z

👋 @bernardsilenou, please update us on how your review is going (this is an automated reminder).

whedon · 2021-09-23T14:08:17Z

👋 @wesleyburr, please update us on how your review is going (this is an automated reminder).

wesleyburr · 2021-09-27T15:23:42Z

The codebase is very clean (as it would have to be, to pass CRAN checks). Nothing to edit in the package or documentation itself, I think, although some modifications should be made to the Readme / community guidelines for the GitHub face and the pkgdown, DOIs added to the references in the paper itself. Three issues opened for the paper author to deal with, then I'm ready to sign off.

danielskatz · 2021-09-27T15:27:18Z

@wesleyburr - please manually create issues in the source repository (https://github.com/ejikeugba/serp) - not here, not using the github convert-to-issue "feature" - this feature doesn't work correctly with JOSS, as the issues are created in the wrong place. (The issues you have created using that feature have been automatically closed, as the JOSS workflow doesn't support them correctly). Also, if you can mention openjournals/joss-reviews#3705 in those issue you create in https://github.com/ejikeugba/serp, they will appear here and then be tracked from this issue.

wesleyburr · 2021-09-27T16:49:11Z

@danielskatz - done!

ejikeugba · 2021-09-30T16:20:55Z

Dear @wesleyburr, thanks for the comments and the suggested issues. I will let you know once I have them all addressed.

ejikeugba · 2021-10-02T11:13:06Z

@wesleyburr, thanks once again for the helpful suggestions, I now have them all addressed. Let me know if there are more things to fix.

ejikeugba · 2021-10-05T07:55:12Z

@Bisaloo, done!

ejikeugba · 2021-10-10T13:23:33Z

@bernardsilenou, thank you for the helpful suggestions. The issues mentioned have all been addressed.

Perhaps, it would make sense to re-generate the pdf once again, since changes are made in it. Thanks!

Bisaloo · 2021-10-25T08:37:14Z

@whedon generate pdf

whedon · 2021-10-25T08:37:42Z

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

Bisaloo · 2021-10-25T08:39:01Z

@whedon check references

whedon · 2021-10-25T08:39:11Z

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

OK DOIs

- 10.1002/9780470594001 is OK
- 10.1111/j.2517-6161.1980.tb01109.x is OK
- 10.2307/2682804 is OK
- 10.1007/978-0-387-84858-7 is OK
- 10.1007/978-3-642-20192-9 is OK
- 10.3390/stats4030037 is OK
- 10.1177/1471082X16642560 is OK
- 10.1111/j.2517-6161.1996.tb02095.x is OK
- 10.18637/jss.v032.i10 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.1080/00401706.2000.10485983 is OK
- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.4137/CIN.S20806 is OK
- 10.18637/jss.v099.i06 is OK
- 10.1080/01621459.2016.1180986 is OK
- 10.1002/bimj.4710310703 is OK
- 10.1002/wics.1296 is OK
- 10.2307/2347760 is OK

MISSING DOIs

- None

INVALID DOIs

- None

bernardsilenou · 2021-10-25T09:57:30Z

@Bisaloo
Responding to #3705 (comment)

I did not find any error related to how the method has been implemented. I also approved the package.

Bisaloo · 2021-10-25T10:29:04Z

@ejikeugba, once ejikeugba/serp#11 is merged, could be please create a new version (edit the DESCRIPTION file and tag the new version on GitHub) and archive the package on, e.g., zenodo?

ejikeugba · 2021-10-25T15:27:14Z

Thanks, @Bisaloo, @wesleyburr, @bernardsilenou for the positive reviews.

The new release version is 0.2.2 and the doi 10.5281/zenodo.5596864

Bisaloo · 2021-10-26T08:07:49Z

@whedon set v0.2.2 as version

whedon · 2021-10-26T08:07:55Z

OK. v0.2.2 is the version.

Bisaloo · 2021-10-26T08:08:29Z

@whedon set 10.5281/zenodo.5596864 as archive

whedon · 2021-10-26T08:08:33Z

OK. 10.5281/zenodo.5596864 is the archive.

Bisaloo · 2021-10-26T08:10:02Z

I'm happy to accept this submission. Congratulations @ejikeugba! 🎉

And thank you again so much @bernardsilenou and @wesleyburr for your valuable help and your time 🙏!

Bisaloo · 2021-10-26T08:10:35Z

@whedon recommend-accept

whedon · 2021-10-26T08:10:38Z

Attempting dry run of processing paper acceptance...

whedon · 2021-10-26T08:11:04Z

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

Check final proof 👉 openjournals/joss-papers#2710

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2710, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon · 2021-10-26T08:11:29Z

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

OK DOIs

- 10.1002/9780470594001 is OK
- 10.1111/j.2517-6161.1980.tb01109.x is OK
- 10.2307/2682804 is OK
- 10.1007/978-0-387-84858-7 is OK
- 10.1007/978-3-642-20192-9 is OK
- 10.3390/stats4030037 is OK
- 10.1177/1471082X16642560 is OK
- 10.1111/j.2517-6161.1996.tb02095.x is OK
- 10.18637/jss.v032.i10 is OK
- 10.1111/j.2517-6161.1996.tb02080.x is OK
- 10.1080/00401706.2000.10485983 is OK
- 10.1111/j.1467-9868.2005.00503.x is OK
- 10.4137/CIN.S20806 is OK
- 10.18637/jss.v099.i06 is OK
- 10.1080/01621459.2016.1180986 is OK
- 10.1002/bimj.4710310703 is OK
- 10.1002/wics.1296 is OK
- 10.2307/2347760 is OK

MISSING DOIs

- None

INVALID DOIs

- None

ejikeugba · 2021-10-26T11:51:49Z

@Bisaloo, thank you very much.
I have gone through the final proof once again, everything looks fine to me.

Thanks once again @wesleyburr and @bernardsilenou for making out time to work on this submission.

kthyng · 2021-10-27T15:42:52Z

@ejikeugba Everything looks ready to go! Nice work team!

kthyng · 2021-10-27T15:43:00Z

@whedon accept deposit=true

whedon · 2021-10-27T15:43:03Z

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

whedon · 2021-10-27T15:43:41Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-10-27T15:43:42Z

🚨🚨🚨 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.03705 joss-papers#2714
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03705
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2021-10-27T15:48:11Z

Congrats on your new publication @ejikeugba!! Many thanks to editor @Bisaloo and reviewers @bernardsilenou and @wesleyburr for your hard work, time, and expertise!!

whedon · 2021-10-27T15:48:15Z

🎉🎉🎉 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.03705/status.svg)](https://doi.org/10.21105/joss.03705)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03705">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03705/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03705/status.svg
   :target: https://doi.org/10.21105/joss.03705

This is how it will look in your documentation:

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whedon added R review TeX labels Sep 9, 2021

whedon assigned Bisaloo Sep 9, 2021

whedon mentioned this issue Sep 9, 2021

[PRE REVIEW]: serp: An R package for smoothing in ordinal regression #3657

Closed

whedon assigned wesleyburr Sep 10, 2021

whedon assigned bernardsilenou Sep 23, 2021

This was referenced Sep 27, 2021

JOSS paper DOIs ejikeugba/serp#3

Closed

Community guidelines / contribution / etc ejikeugba/serp#2

Closed

Readme - dependencies ejikeugba/serp#1

Closed

Bisaloo mentioned this issue Oct 3, 2021

Make pkgdown website more discoverable ejikeugba/serp#6

Closed

bernardsilenou mentioned this issue Oct 7, 2021

Suggestion related to the manuscript ejikeugba/serp#7

Closed

Bisaloo mentioned this issue Oct 25, 2021

Proofs for JOSS ejikeugba/serp#11

Merged

whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Oct 26, 2021

whedon added accepted published Papers published in JOSS labels Oct 27, 2021

kthyng closed this as completed Oct 27, 2021

editorialbot mentioned this issue Sep 27, 2024

[PRE REVIEW]: sleev: An R Package for Semiparametric Likelihood Estimation with Errors in Variables #7297

Closed

[REVIEW]: serp: An R package for smoothing in ordinal regression #3705

[REVIEW]: serp: An R package for smoothing in ordinal regression #3705

Comments

whedon commented Sep 9, 2021 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @bernardsilenou

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @wesleyburr

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 9, 2021

whedon commented Sep 9, 2021

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Bisaloo commented Sep 20, 2021

Bisaloo commented Sep 22, 2021

whedon commented Sep 22, 2021

bernardsilenou commented Sep 22, 2021 via email

whedon commented Sep 23, 2021

whedon commented Sep 23, 2021

wesleyburr commented Sep 27, 2021

danielskatz commented Sep 27, 2021

wesleyburr commented Sep 27, 2021

ejikeugba commented Sep 30, 2021

ejikeugba commented Oct 2, 2021

ejikeugba commented Oct 5, 2021

ejikeugba commented Oct 10, 2021

Bisaloo commented Oct 25, 2021

whedon commented Oct 25, 2021

Bisaloo commented Oct 25, 2021

whedon commented Oct 25, 2021

bernardsilenou commented Oct 25, 2021

Bisaloo commented Oct 25, 2021

ejikeugba commented Oct 25, 2021

Bisaloo commented Oct 26, 2021

whedon commented Oct 26, 2021

Bisaloo commented Oct 26, 2021

whedon commented Oct 26, 2021

Bisaloo commented Oct 26, 2021

Bisaloo commented Oct 26, 2021

whedon commented Oct 26, 2021

whedon commented Oct 26, 2021

whedon commented Oct 26, 2021

ejikeugba commented Oct 26, 2021

kthyng commented Oct 27, 2021

kthyng commented Oct 27, 2021

whedon commented Oct 27, 2021

whedon commented Oct 27, 2021

whedon commented Oct 27, 2021

kthyng commented Oct 27, 2021

whedon commented Oct 27, 2021

whedon commented Sep 9, 2021 •

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