[REVIEW]: ordPens: An R package for Selection, Smoothing and Principal Components Analysis for Ordinal Variables

whedon commented 3 years ago

Submitting author: @ahoshiyar (Aisouda Hoshiyar) Repository: https://github.com/ahoshiyar/ordPens Version: 1.0.1 Editor: @osorensen Reviewer: @fartist, @FranjoIM, @mingzehuang Archive: 10.5281/zenodo.5718572

:warning: JOSS reduced service mode :warning:

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/2418101c27f855d290a5da28bcee0ea5"><img src="https://joss.theoj.org/papers/2418101c27f855d290a5da28bcee0ea5/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/2418101c27f855d290a5da28bcee0ea5/status.svg)](https://joss.theoj.org/papers/2418101c27f855d290a5da28bcee0ea5)

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

@fartist & @FranjoIM & @mingzehuang, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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 ✨

Review checklist for @fartist

✨ 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ahoshiyar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @FranjoIM

✨ 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ahoshiyar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 @mingzehuang

✨ 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

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@ahoshiyar) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @fartist, @FranjoIM, @mingzehuang it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

watching

You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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

@whedon commands

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

@whedon generate pdf

whedon commented 3 years ago

Wordcount for paper.md is 1310

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.08 s (238.6 files/s, 65329.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              1              0             46           1522
R                                9            332            120           1463
TeX                              2             96              2            808
Rmd                              4            204            351            249
Markdown                         4             70              0            214
-------------------------------------------------------------------------------
SUM:                            20            702            519           4256
-------------------------------------------------------------------------------

Statistical information for the repository '418e8a0ed3ff7df61d621739' was
gathered on 2021/10/15.
No commited files with the specified extensions were found.

whedon commented 3 years ago

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

OK DOIs

- 10.1111/j.1467-9876.2010.00753.x is OK
- 10.1214/11-EJS661 is OK
- 10.1111/j.1751-5823.2009.00088.x is OK
- 10.1214/10-aoas355 is OK
- 10.1007/s13253-014-0170-5 is OK
- 10.1515/sagmb-2015-0091 is OK
- 10.31234/osf.io/9qkhj is OK
- 10.1207/s15327906mbr0102_10 is OK
- 10.3390/su11143907 is OK
- 10.1016/s0167-9473(97)00038-8 is OK
- 10.1007/978-981-10-0159-8_2 is OK
- 10.1002/wics.1279 is OK
- 10.1007/bfb0092976 is OK
- 10.1007/bf02591962 is OK
- 10.1007/bf02293871 is OK
- 10.1007/S11336-013-9343-3 is OK
- 10.1007/s11336-018-9623-z is OK
- 10.1177/1471082X16642560 is OK
- 10.4324/9781315128948-36 is OK
- 10.1111/j.1467-9868.2007.00646.x is OK
- 10.1214/ss/1038425655 is OK
- 10.1111/j.1467-9868.2007.00627.x is OK
- 10.1111/j.1467-9868.2005.00490.x is OK
- 10.1111/j.1467-9868.2005.00532.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

FranjoIM commented 3 years ago

Overall looks good, there are a couple of (relatively) minor points I would like the author to address:

osorensen commented 3 years ago

Thanks for working so quickly, @FranjoIM. @ahoshiyar, feel free to start responding to the issues raised by @FranjoIM whenever you like.

mingzehuang commented 3 years ago

Overall it looks great to see a package dealing with ordinal data without need to specify each cases (numbers of ordinal levels) specifically. I'm reading details, but now I have some suggestion on CODE OF CONDUCT and CONTRIBUTING GUIDELINE

mingzehuang commented 3 years ago

It looks easy and smooth to install your package from GitHub. I would suggest you providing a bit more guidance for new users on README.md Installation Guidance on README.md

mingzehuang commented 3 years ago

It looks nice and straightforward to use penalty terms to deal with ordinal data. It's probably interesting to see if there is something comparable between this penalty term method with other methods like Gaussian copula model for latent correlation (of ordinal data)

whedon commented 3 years ago

:wave: @fartist, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @mingzehuang, please update us on how your review is going (this is an automated reminder).

whedon commented 3 years ago

:wave: @FranjoIM, please update us on how your review is going (this is an automated reminder).

FranjoIM commented 3 years ago

I am still waiting on @ahoshiyar to address the open issues.

fartist commented 3 years ago

I am reviewing it right now. Sent from Mail for Windows From: Franjo IvankovicSent: Wednesday, November 3, 2021 9:37 PMTo: openjournals/joss-reviewsCc: Feeeeeeeeeeng; MentionSubject: Re: [openjournals/joss-reviews] [REVIEW]: ordPens: An R package for Selection, Smoothing and Principal Components Analysis for Ordinal Variables (#3828) I am still waiting on @ahoshiyar to address the open issues.—You are receiving this because you were mentioned.Reply to this email directly, view it on GitHub, or unsubscribe.Triage notifications on the go with GitHub Mobile for iOS or Android.

osorensen commented 3 years ago

@fartist @FranjoIM , thanks for responding, and sorry about the automated reminder. I unfortunately cannot turn it off.

osorensen commented 3 years ago

@ahoshiyar can you please update us on how it is going addressing the issues raised by the reviewers in the source repository?

FranjoIM commented 3 years ago

I have completed the review at this point. The author has addressed my concerns, and pending the review of the other two reviewers, I am recommending this paper for acceptance.

osorensen commented 3 years ago

Thanks a lot for your work, @FranjoIM!

ahoshiyar commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

ahoshiyar commented 3 years ago

Thank you a lot @FranjoIM !

ahoshiyar commented 3 years ago

Dear all, note that the Statement of Need section has been updated (adressing a very interesting comment from @mingzehuang) discussing potential future work/related work.

mingzehuang commented 3 years ago

Thank you, @ahoshiyar ! It looks perfectly address my concern! I'm going to finish reviewing the rest of parts ASAP:)

osorensen commented 3 years ago

@fartist, could you please update us on how it's going with your review?

fartist commented 3 years ago

Please find my review at https://github.com/ahoshiyar/ordPens/issues/9 @ahoshiyar - solid work!

osorensen commented 3 years ago

Thank you, @ahoshiyar ! It looks perfectly address my concern! I'm going to finish reviewing the rest of parts ASAP:)

@mingzehuang, thanks for your great efforts so far! Do you have any other concerns to this submission, or have they been addressed? If so, could you please update your checklist at the top of this page?

mingzehuang commented 3 years ago

Great work @ahoshiyar ! My last comment is to generate automated tests which is required by the checklist. Tests

ahoshiyar commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

mingzehuang commented 2 years ago

I have completed the review. The author has perfectly addressed my concerns, I am recommending this paper for acceptance:)

osorensen commented 2 years ago

@fartist, there is one unchecked box in your review checklisit at the top of this thread, regarding references. Could you please check if this issue has now been resolved?

osorensen commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

fartist commented 2 years ago

Thanks - @osorensen, have completed the review. I have no further comments - @ahoshiyar did a great job addressing my concerns - I recommend it to be accepted.

osorensen commented 2 years ago

Thanks a lot to @fartist, @FranjoIM, and @mingzehuang for their reviews. You work is very much appreciated!

@ahoshiyar, I will now read through the paper once again, and get back to you if I have any furter comments. In the meantime, could you please do the following:

[ ] 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.

ahoshiyar commented 2 years ago

Thank you so much for your comments, @osorensen! The tagged version is 1.0.1 & Zenodo DOI is 10.5281/zenodo.5718572

ahoshiyar commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

osorensen commented 2 years ago

@whedon set 10.5281/zenodo.5718572 as arcive

whedon commented 2 years ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

osorensen commented 2 years ago

@whedon set 10.5281/zenodo.5718572 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5718572 is the archive.

osorensen commented 2 years ago

@whedon set 1.0.1 as version

whedon commented 2 years ago

OK. 1.0.1 is the version.

osorensen commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.1111/j.1467-9876.2010.00753.x is OK
- 10.1214/11-EJS661 is OK
- 10.1111/j.1751-5823.2009.00088.x is OK
- 10.1214/10-aoas355 is OK
- 10.1007/s13253-014-0170-5 is OK
- 10.1515/sagmb-2015-0091 is OK
- 10.31234/osf.io/9qkhj is OK
- 10.1207/s15327906mbr0102_10 is OK
- 10.3390/su11143907 is OK
- 10.1016/s0167-9473(97)00038-8 is OK
- 10.1007/978-981-10-0159-8_2 is OK
- 10.1002/wics.1279 is OK
- 10.1007/bfb0092976 is OK
- 10.1007/bf02591962 is OK
- 10.1007/bf02293871 is OK
- 10.1007/S11336-013-9343-3 is OK
- 10.1007/s11336-018-9623-z is OK
- 10.1177/1471082X16642560 is OK
- 10.4324/9781315128948-36 is OK
- 10.1111/j.1467-9868.2007.00646.x is OK
- 10.1214/ss/1038425655 is OK
- 10.1111/j.1467-9868.2007.00627.x is OK
- 10.1111/j.1467-9868.2005.00490.x is OK
- 10.1111/j.1467-9868.2005.00532.x is OK
- 10.21105/joss.03634 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2762

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2762, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

Kevin-Mattheus-Moerman commented 2 years ago

@ahoshiyar I have proofread your paper which seems in order. However the ZENODO archive needs changes as listed below:

[ ] ~~Please amend the license on the ZENODO archive (you have to do this manually) to match your software license: https://github.com/ahoshiyar/ordPens/blob/master/LICENSE, it currently lists cc-by.~~

openjournals / joss-reviews