[REVIEW]: ALUES: An R package for Agricultural Land Use Evaluation System

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@alstat@fabian-s<!--end-editor-- Reviewers: @corybrunson, @kuesterc9 Archive: 10.5281/zenodo.6529873

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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

@corybrunson & @kuesterc9, 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 @corybrunson

📝 Checklist for @kuesterc9

editorialbot commented 2 years ago

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editorialbot commented 2 years ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.48 s (1119.4 files/s, 148281.0 lines/s)
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R                              242            261           5922           3347
C++                              6             26             55            693
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JavaScript                       4             64             34            266
Rmd                              8             61            405            223
Markdown                         5             43              0            211
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SVG                              2              0              1             29
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SUM:                           540          13706          10010          47813
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gitinspector failed to run statistical information for the repository

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.envsoft.2003.10.006 is OK
- 10.1016/j.compag.2013.02.003 is OK
- 10.1080/10618600.1996.10474713 is OK
- 10.1111/j.1475-2743.1991.tb00881.x is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1016/S0198-97150100031-X is INVALID
- 10.1016/S0019-99586590241-X is INVALID

editorialbot commented 2 years ago

Wordcount for paper.md is 949

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

👋🏼 @alstat @corybrunson @kuesterc9 this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers please first create your checklist by running this command in a separate comment to create the checklist:

@editorialbot generate my checklist

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#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 if you have any questions/concerns.

fabian-s commented 2 years ago

@alstat please also correct the two invalid DOIs in your references (see editorialbot-comment above)

corybrunson commented 2 years ago

Review checklist for @corybrunson

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/alstat/ALUES?
[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 (@alstat) 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?

alstat commented 2 years ago

@alstat please also correct the two invalid DOIs in your references (see editorialbot-comment above)

Noted on this. Thanks.

corybrunson commented 2 years ago

@fabian-s FYI i checked roughly half the boxes on my checklist yesterday and today found them all unchecked. Moreover, i find myself now unable to check boxes. Do you have an idea of what might be wrong? I will try logging out and back in, etc.

Update: I restarted my browser and the checks are restored and editable. I'm sorry for the alarm, and i'll watch out for possible causes.

corybrunson commented 2 years ago

@fabian-s i have completed the first phase of my review.

@alstat i'll be glad to respond to feedback on the issues i raised and will check the remaining boxes to complete my review as they are addressed.

Thank you both!

fabian-s commented 2 years ago

thanks @corybrunson !
glad the checklist-problem seems to have solved itself! :)

fabian-s commented 2 years ago

@kuesterc9 , do you have any questions before you start your review? JOSS aims for short turn-around times, if I can help speed up the process let me know.

kuesterc9 commented 2 years ago

Review checklist for @kuesterc9

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/alstat/ALUES?
[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 (@alstat) 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?

fabian-s commented 2 years ago

@alstat could you give us a brief update on your progress resolving the issues pointed out by the reviewers?

fabian-s commented 2 years ago

@alstat please adress the issues raised by the reviewers and let us know here in the thread your timeframe for doing so before the week-end

fabian-s commented 2 years ago

@editorialbot remind @alstat in 2 days

editorialbot commented 2 years ago

Reminder set for @alstat in 2 days

fabian-s commented 2 years ago

@editorialbot remind @fabian-s in 5 days

editorialbot commented 2 years ago

@fabian-s doesn't seem to be a reviewer or author for this submission.

alstat commented 2 years ago

@fabian-s, sorry, I was a bit loaded, but will work on it today on the remaining issues.

editorialbot commented 2 years ago

:wave: @alstat, please update us on how things are progressing here (this is an automated reminder).

fabian-s commented 2 years ago

sorry, I was a bit loaded, but will work on it today on the remaining issues.

yes, please do so now, this has been inactive for a rather long time.

corybrunson commented 2 years ago

@fabian-s my concerns have been addressed, pending re-generation of the PDF. Thank you, @alstat, for the detailed responses!

alstat commented 2 years ago

Hi @fabian-s,

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

OK DOIs

- 10.1016/j.envsoft.2003.10.006 is OK
- 10.1016/j.compag.2013.02.003 is OK
- 10.1080/10618600.1996.10474713 is OK
- 10.1111/j.1475-2743.1991.tb00881.x is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1016/S0198-97150100031-X is INVALID
- 10.1016/S0019-99586590241-X is INVALID

The invalid DOIs here are due to missing parentheses. So,

10.1016/S0198-97150100031-X # invalid
10.1016/S0198-9715(01)00031-X # correct

and,

10.1016/S0019-99586590241-X # invalid
10.1016/S0019-9958(65)90241-X # correct

The correct DOIs are the ones in the paper, not sure why the parentheses are omitted when checkin. For reference, here are the complete URLs for the two DOIs above:

https://doi.org/10.1016/S0198-9715(01)00031-X
https://doi.org/10.1016/S0019-9958(65)90241-X

Not sure how to resolve this.

danielskatz commented 2 years ago

👋 @xuanxu - Is this something you can fix?

xuanxu commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.envsoft.2003.10.006 is OK
- 10.1016/j.compag.2013.02.003 is OK
- 10.1080/10618600.1996.10474713 is OK
- 10.1016/S0198-9715(01)00031-X is OK
- 10.1016/S0019-9958(65)90241-X is OK
- 10.1111/j.1475-2743.1991.tb00881.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

xuanxu commented 2 years ago

Fixed!

danielskatz commented 2 years ago

thanks!

alstat commented 2 years ago

Thank you! Let me know on the next steps or any pending tasks I have to address.

fabian-s commented 2 years ago

@kuesterc9 you left the checkmarks for "automated tests" and "community guidelines" out -- do you have remaining points of criticism or have your concerns been addressed in the meantime?

fabian-s commented 2 years ago

@editorialbot generate pdf

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:

kuesterc9 commented 2 years ago

@kuesterc9 you left the checkmarks for "automated tests" and "community guidelines" out -- do you have remaining points of criticism or have your concerns been addressed in the meantime?

I think everything is now fine! ;-)

fabian-s commented 2 years ago

@alstat

please take a look at the issue I opened re. best practices for scientific software in R and take a look at the PR suggesting some minor edits to the paper.

Addressing https://github.com/alstat/ALUES/issues/24 is not necessary for JOSS publication. IMO would still be a good idea that would improve your package.

alstat commented 2 years ago

Thank you, @fabian-s. Already merged alstat/ALUES#25, and noted on the best practices.

fabian-s commented 2 years ago

@editorialbot check references

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.envsoft.2003.10.006 is OK
- 10.1016/j.compag.2013.02.003 is OK
- 10.1080/10618600.1996.10474713 is OK
- 10.1016/S0198-9715(01)00031-X is OK
- 10.1016/S0019-9958(65)90241-X is OK
- 10.1111/j.1475-2743.1991.tb00881.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

fabian-s commented 2 years ago

@editorialbot generate pdf

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

@alstat Seems like we're good to go here :rocket:

At this point could you:

[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 reommending acceptance of the submission.

alstat commented 2 years ago

Hi @fabian-s, below is the link of the archived software in Zenodo, following the correct metadata:

https://zenodo.org/record/6529873#.YniNtRNBx-o

Here is the DOI of the archived version: 10.5281/zenodo.6529873

fabian-s commented 2 years ago

Great -- please also make a tagged release of your software, and list the version tag of the archived version here Link to Github Docs so I can recommend acceptance of your paper.

alstat commented 2 years ago

Hi @fabian-s, I have it here: https://github.com/alstat/ALUES/releases/tag/v0.2.1

fabian-s commented 2 years ago

@editorialbot set 10.5281/zenodo.6529873 as archive

editorialbot commented 2 years ago

Done! Archive is now 10.5281/zenodo.6529873

fabian-s commented 2 years ago

@editorialbot recommend-accept

editorialbot commented 2 years ago

Attempting dry run of processing paper acceptance...

editorialbot commented 2 years ago

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

OK DOIs

- 10.1016/j.envsoft.2003.10.006 is OK
- 10.1016/j.compag.2013.02.003 is OK
- 10.1080/10618600.1996.10474713 is OK
- 10.1016/S0198-9715(01)00031-X is OK
- 10.1016/S0019-9958(65)90241-X is OK
- 10.1111/j.1475-2743.1991.tb00881.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

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