[REVIEW]: UBayFS: An R Package for User Guided Feature Selection

editorialbot commented 1 year ago

Submitting author: !--author-handle-->@annajenul@osorensen<!--end-editor-- Reviewers: @dhvalden, @aaronpeikert, @EugeneHao Archive: 10.5281/zenodo.7554373

Status

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Markdown: [![status](https://joss.theoj.org/papers/a7ebe73cf7176317c9ebfe1385dcae51/status.svg)](https://joss.theoj.org/papers/a7ebe73cf7176317c9ebfe1385dcae51)

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

@dhvalden & @aaronpeikert & @EugeneHao, 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 @aaronpeikert

📝 Checklist for @EugeneHao

📝 Checklist for @dhvalden

editorialbot commented 1 year ago

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 commented 1 year ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (753.5 files/s, 138894.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               13            320            283           1972
TeX                              2             66             10            501
Markdown                         3             78              0            213
Rmd                              2             84            221            122
CSS                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                            21            548            514           2809
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

Wordcount for paper.md is 1382

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:

editorialbot commented 1 year ago

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

OK DOIs

- None

MISSING DOIs

- 10.1109/access.2021.3126429 may be a valid DOI for title: RENT—Repeated Elastic Net Technique for Feature Selection
- 10.1007/s10994-022-06221-9 may be a valid DOI for title: A User-Guided Bayesian Framework for Ensemble Feature Selection in Life Science Applications (UBayFS)
- 10.1016/j.simpa.2022.100414 may be a valid DOI for title: Rdimtools: An R package for dimension reduction and intrinsic dimension estimation
- 10.1093/bioinformatics/btt383 may be a valid DOI for title: mRMRe: an R package for parallelized mRMR ensemble feature selection
- 10.1016/j.knosys.2016.11.017 may be a valid DOI for title: Ensemble feature selection: Homogeneous and heterogeneous approaches

INVALID DOIs

- None

EugeneHao commented 1 year ago

Review checklist for @EugeneHao

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/annajenul/UBayFS?
[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 (@annajenul) 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?

EugeneHao commented 1 year ago

@editorialbot generate pdf

EugeneHao commented 1 year ago

@editorialbot commands

editorialbot commented 1 year ago

Hello @EugeneHao, here are the things you can ask me to do:


# List all available commands
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@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
@editorialbot set joss-paper as branch

# Generates the pdf paper
@editorialbot generate pdf

# Generates a LaTeX preprint file
@editorialbot generate preprint

# Get a link to the complete list of reviewers
@editorialbot list reviewers

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:

aaronpeikert commented 1 year ago

Review checklist for @aaronpeikert

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/annajenul/UBayFS?
[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 (@annajenul) 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?

aaronpeikert commented 1 year ago

I have only gotten around to take a quick look at the installation, dependencies, and automated testing:

I'll check back in two weeks to do the rest.

osorensen commented 1 year ago

Thanks @aaronpeikert!

FYI @annajenul, you're welcome to start addressing these issues right away, as the review process in JOSS is supposed to be iterative.

osorensen commented 1 year ago

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

EugeneHao commented 1 year ago

@osorensen I just updated the checklist. Thank you for the reminder!

aaronpeikert commented 1 year ago

@annajenul I'd like to review the software's functionality more in-depth (by, e.g. simulating some data), but this requires more time than I have this week. Do you prefer that I take an in-depth look, which might lengthen the review by 2-3 weeks or a more cursory look (fitting some models to data where I do not know the true answers)?

osorensen commented 1 year ago

@aaronpeikert, I'd like to chime in as an editor here and say that it would be very appreciated if you could take an in-depth look, even though it takes additional time.

aaronpeikert commented 1 year ago

Thank you, @osorensen. I want to be mindful that @annajenul might have higher pressure to face as an ECR regarding the timeliness of reviews. In any case, I take the responsibility of reviewing the software seriously—just a question of going the extra mile.

annajenul commented 1 year ago

Thank you, @aaronpeikert We would appreciate thorough feedback!

aaronpeikert commented 1 year ago

Than you‘ll get it (but give me some time).

osorensen commented 1 year ago

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

dhvalden commented 1 year ago

Review checklist for @dhvalden

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/annajenul/UBayFS?
[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 (@annajenul) 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?

dhvalden commented 1 year ago

Dear @osorensen Thanks for the reminder, I'm updating the check-list now and running the installation and examples.

dhvalden commented 1 year ago

So far the installation seems to be running ok with the exception of this issue:

[x] https://github.com/annajenul/UBayFS/issues/22#issue-1479897544

dhvalden commented 1 year ago

As an update, I can confirm the core functionality with the exception of the shiny dashboard. I listed a couple of very minor improvements in here:

[x] https://github.com/annajenul/UBayFS/issues/23#issue-1482556305 But it seems that everything runs smoothly.

dhvalden commented 1 year ago

I can confirm that the Shiny App works under my set-up. I found some small issues with the app, but they do not affect the main functionality:

[x] https://github.com/annajenul/UBayFS/issues/24#issue-1484910999

Additionally, there is some small issue with the unstated handling of NAs in the calculations that I think should be more transparent to avoid confusion in the user.

[x] https://github.com/annajenul/UBayFS/issues/25#issue-1484974413

I can also confirm that the test functionality works and all the described tests passed with OK status. Finally, I would like to see mentions in the paper of just a couple of examples of packages or tools with the same functionality, just to have a comparison. If this final point is addressed I would declare myself satisfied and close the review @osorensen.

osorensen commented 1 year ago

@EugeneHao and @aaronpeikert, could you please update us on how it's going with your reviews, and whether your points have been properly addressed?

aaronpeikert commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

⚠️ An error happened when generating the pdf.

That was strange. I tried to issue the command once more to see if it was only temporary. If the problem remains I'll try to figure out what has happened.

editorialbot commented 1 year ago

:warning: An error happened when generating the pdf.

osorensen commented 1 year ago

@openjournals/dev could you please help us figure out why generating the pdf fails?

xuanxu commented 1 year ago

The error happens because the bot is trying to find the paper in the master branch but that branch does not exist (I guess it's been renamed recently?)

osorensen commented 1 year ago

@editorialbot set main as branch

editorialbot commented 1 year ago

Done! branch is now main

osorensen 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:

osorensen commented 1 year ago

Now the pdf generation should work @aaronpeikert.

aaronpeikert commented 1 year ago

Thanks for working this out @xuanxu & @osorensen .

annajenul commented 1 year ago

Dear @osorensen, @aaronpeikert, and @EugeneHao, We thank you for your constructive feedback on our software so far. Your comments already helped us a lot to improve the package. Could you please inform us when you anticipate finalizing the review process? Thank you very much!

osorensen commented 1 year ago

@aaronpeikert, I notice the unchecked item on your checklist regards documentation, but cannot see any issue about this in the source repository. Could you please elaborate, so @annajenul knows what to fix? Thank you.

EugeneHao commented 1 year ago

My issue has been resolved. The example and shiny app now work well on my machine.

aaronpeikert commented 1 year ago

Good to go from my side!

osorensen commented 1 year ago

Thanks to both of you!

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen 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

- 10.1109/ACCESS.2021.3126429 is OK
- 10.1007/s10994-022-06221-9 is OK
- 10.18637/jss.v053.i04 is OK
- 10.1016/j.simpa.2022.100414 is OK
- 10.1093/bioinformatics/btt383 is OK
- 10.1016/j.knosys.2016.11.017 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:

annajenul commented 1 year ago

Thank you very much for your time and the great input from your reviews, @aaronpeikert, @dhvalden, and @EugeneHao! Thank you for handling the reviewing process @osorensen :smiley:

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