[REVIEW]: enetLTS: Robust and Sparse Methods for High Dimensional Linear, Binary, and Multinomial Regression

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@fatmasevinck@fabian-s<!--end-editor-- Reviewers: @mcavs, @marastadler Archive: 10.5281/zenodo.7598948

Status

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Markdown: [![status](https://joss.theoj.org/papers/571e01add8e8da527504e4a2f83a1335/status.svg)](https://joss.theoj.org/papers/571e01add8e8da527504e4a2f83a1335)

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

@mcavs & @marastadler, 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 @fabian-s 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 @marastadler

📝 Checklist for @mcavs

editorialbot commented 2 years ago

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

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1568.7 files/s, 150226.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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R                               38            424            161           2925
Markdown                         3            140              0            277
TeX                              1             17              0            135
YAML                             1              5              7             27
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SUM:                            43            586            168           3364
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gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

Wordcount for paper.md is 1924

editorialbot commented 2 years ago

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

OK DOIs

- 10.1214/12-AOAS575 is OK
- 10.21105/joss.03786 is OK
- 10.18637/jss.v033.i01 is OK
- 10.1111/biom.13553 is OK
- 10.3390/stats4030040 is OK
- 10.1016/j.chemolab.2017.11.017 is OK
- 10.48550/arXiv.2205.11835 is OK
- 10.1007/s11634-021-00465-4 is OK
- 10.1177/09622802211072456 is OK
- 10.1158/0008-5472.can-12-1370 is OK
- 10.1177/0962280218794722 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot 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:

fabian-s commented 2 years ago

👋🏼 @fatmasevinck @mcavs @marastadler this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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#REVIEW_NUMBER 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 EditorialBot (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 (@fabian-s ) if you have any questions/concerns. Thank you for supporting JOSS with your fair and dilligent reviews!

marastadler commented 2 years ago

Review checklist for @marastadler

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 https://github.com/fatmasevinck/enetLTS?
[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 (@fskurnaz) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

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

mcavs commented 2 years ago

Review checklist for @mcavs

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 https://github.com/fatmasevinck/enetLTS?
[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 (@fskurnaz) 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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

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

fabian-s commented 2 years ago

hi @marastadler @mcavs, thanks for filling out the review checklists.

please help @fatmasevinck adress the problems you have identified by adding some more specific comments on what's missing (and how to fix them, if you have ideas), preferably by opening corresponding review issues or pull requests at https://github.com/fatmasevinck/enetLTS/issues and linking them back to this issue by including See openjournals/joss-reviews#4773 in the text of the issue(s)/PRs you open.

@fatmasevinck please start adressing the problems pointed out by the reviewers as soon as possible - what is your timeframe for doing so?

marastadler commented 2 years ago

Hi @fatmasevinck, I like the general structure of your paper. The text itself still needs a little polishing.

In some places the quotation is in brackets, although it is part of the sentence (see, for example, lines 26/27, 42, 71, 92/93).
- Sometimes spaces are missing in the text (e.g. enetLTS()function (line 87), nCsteps (line 57)).
- Also, the manuscript should be double-checked for typos (like fuit instead of fruit, e.g. 105).

marastadler commented 2 years ago

@fatmasevinck You add plots in Readme.md in the multinomial regression section that are not in the manuscript. When plotting the coefficients in the first of these plots, the x-axis label is difficult to read. You could sort the features by importance and/or show only a subset of the coefficients.

marastadler commented 2 years ago

@fatmasevinck the community guidelines are missing. One option to add such guidelines can be seen here: https://github.com/fabian-sp/GGLasso.

marastadler commented 2 years ago

@fatmasevinck in the chapter "related software" you name a few packages. It would be useful to elaborate a bit more on how these packages differ from enetLTS (e.g. would the package pense in the linear model case give the same results as enetLTS, or are they different and, if so, why?)

fabian-s commented 2 years ago

hi @mcavs, thank you for filling out the review checklist.

Please help @fatmasevinck adress the problems you have identified by adding some more specific comments on what's missing (and how to fix them, if you have ideas), preferably by opening corresponding review issues or pull requests at https://github.com/fatmasevinck/enetLTS/issues and linking them back to this issue by including See openjournals/joss-reviews#4773 in the text of the issue(s)/PRs you open.

fabian-s commented 2 years ago

@fatmasevinck please start adressing the problems pointed out by the reviewers as soon as possible - what is your timeframe for doing so?

fabian-s commented 1 year ago

hi @fatmasevinck this is another reminder to please start addressing the problems pointed out by the reviewers as soon as possible and to let us know what your timeframe for doing so looks like. If we do not receive any reply to this message from you before Friday, Oct 14 I will unfortunately have to recommend rejection of this submission.

fabian-s commented 1 year ago

hi @mcavs, thank you for filling out the review checklist. JOSS aims for collaborative and constructive style reviews so I would like to ask you to please help the authors address the problems you have identified by

adding some more specific comments on what's missing (and how to fix them, if you have ideas),
preferably by opening corresponding review issues or pull requests at https://github.com/fatmasevinck/enetLTS/issues and
linking them back to this issue by including See openjournals/joss-reviews#4773 in the text of the issue(s)/PRs you open.

Thank you for supporting JOSS!

fabian-s commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

as far as I can determine given the lack of communication by fatmasevinck, the only outstanding issue here now is

/fatmasevinck/enetLTS/issues/16 : adding a contributing.md or similar as community guidelines.

@mcavs @marastadler is this assessment correct?

mcavs commented 1 year ago

@fabian-s The issues that I commented on https://github.com/fatmasevinck/enetLTS/issues/15 are solved by @fatmasevinck. It is ok for me.

marastadler commented 1 year ago

@fabian-s some of my comments have not been addressed yet. I have specified what is still missing in https://github.com/fatmasevinck/enetLTS/issues/14

fatmasevinck commented 1 year ago

Dear @fabian-s

I am trying to do my best now.

Many thanks for your effort.

Sevinç

fabian-s commented 1 year ago

@editorialbot generate pdf

fabian-s commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1214/12-AOAS575 is OK
- 10.21105/joss.03786 is OK
- 10.18637/jss.v033.i01 is OK
- 10.1111/biom.13553 is OK
- 10.3390/stats4030040 is OK
- 10.1016/j.chemolab.2017.11.017 is OK
- 10.48550/arXiv.2205.11835 is OK
- 10.1007/s11634-021-00465-4 is OK
- 10.1177/09622802211072456 is OK
- 10.1158/0008-5472.can-12-1370 is OK
- 10.1177/0962280218794722 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

@editorialbot generate pdf

fabian-s commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1214/12-AOAS575 is OK
- 10.21105/joss.03786 is OK
- 10.18637/jss.v033.i01 is OK
- 10.1111/biom.13553 is OK
- 10.3390/stats4030040 is OK
- 10.1016/j.chemolab.2017.11.017 is OK
- 10.48550/arXiv.2205.11835 is OK
- 10.1007/s11634-021-00465-4 is OK
- 10.1177/09622802211072456 is OK
- 10.1158/0008-5472.can-12-1370 is OK
- 10.1177/0962280218794722 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

fabian-s commented 1 year ago

Seems like this is finally publishable -- @fatmasevinck, at this point please:

[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] 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.
[x] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of your submission, at last.

fatmasevinck commented 1 year ago

Dear @fabian-s Here is the DOI number: 10.5281/zenodo.7597731

Many thanks for your kind effort and help. Best,

fabian-s commented 1 year ago

sorry but that's not how these deposits are supposed to look -- obviously, your archival deposit must be identical to the Git repo that was reviewed by us -- same folder structure, all the files incl. the paper, etc, etc, and not just an unsorted, incomplete dump of program files…..

Pls do take the time to take a look at any other published JOSS paper to understand how this is supposed to look (e.g https://zenodo.org/record/7554373 for https://joss.theoj.org/papers/10.21105/joss.04848) -- you could save us all a lot of back and forth by doing a little more due dilligence or asking a more technical person from your institution to help you out if necessary.

pls remember we also need a tagged release on github so we can finally wrap this up.

fatmasevinck commented 1 year ago

Thanks for your answer and understanding.

I have mad the tagged release yesterday (https://github.com/fatmasevinck/enetLTS/releases/tag/v0.1.0)

Now my archival deposit is identical to Git repo (https://zenodo.org/record/7598948#.Y9ur4exBxo4)

Hope that everything is ok now. Best @fabian-s, Sevinç

fabian-s commented 1 year ago

please adjust the license of your zenodo repo (currently CC Attribution 4.0) so it matches that of your Github repo (GNU General Public License v3.0.)

fatmasevinck commented 1 year ago

It is done.

fabian-s commented 1 year ago

no, it's not :clown_face: please do not waste any more time with this....

fatmasevinck commented 1 year ago

🙈

fabian-s commented 1 year ago

@fatmasevinck : please fix this now so we can all move on, at last
I've never encountered this level of negligence, disorganization and avoidable delays in a JOSS review before and I'm running out of patience, in case you can't tell.

openjournals / joss-reviews