editorialbot commented 1 year ago

Submitting author: !--author-handle-->@JeremyGelb@martinfleis<!--end-editor-- Reviewers: @ljwolf, @naeemkh Archive: 10.5281/zenodo.8316593

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/c9a31248bf2d9d649e47d53b7424a2bd/status.svg)](https://joss.theoj.org/papers/c9a31248bf2d9d649e47d53b7424a2bd)

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

@nuest & @ljwolf, 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 @martinfleis 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 @ljwolf

📝 Checklist for @Naeemkh

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=0.24 s (947.6 files/s, 188630.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                           132           3611            428          20806
R                               46           1153           3125           4668
JavaScript                      10            626            990           3018
C++                              7            210            772           1572
Rmd                              6            456            672            717
Markdown                         6            216              0            475
CSS                              6            102             61            466
XML                              1              0              0            387
YAML                             6             29             16            249
TeX                              2             13              0            144
Sass                             1              4              0             71
JSON                             1              3              0             68
C/C++ Header                     2             20              4             24
SVG                              1              0              1             11
-------------------------------------------------------------------------------
SUM:                           227           6443           6069          32676
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 1 year ago

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

OK DOIs

- 10.4000/cybergeo.36414 is OK
- 10.1016/j.patcog.2006.07.011 is OK
- 10.1016/j.dsp.2012.09.016 is OK
- 10.1007/s00180-018-0791-1 is OK
- 10.2307/622300 is OK
- 10.1080/13658810600665111 is OK
- 10.1111/j.1538-4632.2006.00689.x is OK
- 10.1016/j.cageo.2015.05.019 is OK
- 10.1016/j.patcog.2011.02.009 is OK
- 10.1016/0167-8655(91)90002-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

Wordcount for paper.md is 1842

martinfleis commented 1 year ago

👋🏼 @JeremyGelb, @nuest, @ljwolf this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers should create checklists with the JOSS requirements using the command @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 small pull requests if needed) on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/5259 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, feel free to start whenever it works for you. Please let me know if any of you require significantly more time. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

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

Thanks!

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:

ljwolf commented 1 year ago

Review checklist for @ljwolf

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/JeremyGelb/geocmeans?
[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 (@JeremyGelb) 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?

martinfleis commented 1 year ago

@editorialbot remind @ljwolf in 2 weeks

editorialbot commented 1 year ago

Reminder set for @ljwolf in 2 weeks

martinfleis commented 1 year ago

@editorialbot remind @nuest in 2 weeks

editorialbot commented 1 year ago

Reminder set for @nuest in 2 weeks

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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

martinfleis commented 1 year ago

Hi @ljwolf and @nuest, could you let me know how's your progress on this review and how much time do you still need? Thanks!

JeremyGelb commented 1 year ago

Dear @martinfleis, @ljwolf and @nuest, I hope that the review process is going well. There has been no activity on this issue for two weeks. Let me know if I can help.

ljwolf commented 1 year ago

Hi @JeremyGelb, it looks fine to me!

Although, I think the vignette would benefit from using sf classes instead of sp, especially since the class of LyonIris will depend on the users' configuration. My default configuration read that as an sf rather than an sp object, so the vignette needed some small changes to execute. But, for users with sp as their default, this should run correctly.

JeremyGelb commented 1 year ago

Hi @ljwolf!

Thank you for completing the review! Could you please indicated me where did you find code samples using sp classes instead of sf? I removed sp, rgdal and maptools from geocmeans dependencies when passing at version 0.2.3 but it is not impossible that I missed something in the documentation.

ljwolf commented 1 year ago

No problem! It's in the "example" in the JOSS paper itself:

https://github.com/JeremyGelb/geocmeans/blob/ef12c5174b0dc6d8a6ad50972dae69b1a39e712f/JOSS/paper.md?plain=1#L163

even though you've updated the actual R vignettes:

https://github.com/JeremyGelb/geocmeans/blob/master/vignettes/introduction.Rmd#L80

JeremyGelb 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:

JeremyGelb commented 1 year ago

I modified the example in the paper and uploaded the new file on github. I also modified a typo in the first figure.

ljwolf commented 1 year ago

Cool, looks fine to me, then!

martinfleis commented 1 year ago

Thank you @ljwolf!

I haven't heard back from @nuest so I'll give them a few more days and try to find a replacement reviewer f that does not change by then.

martinfleis commented 1 year ago

@editorialbot remove @nuest from reviewers

@JeremyGelb I am looking for a new reviewer. Sorry for the inconvenience.

editorialbot commented 1 year ago

@nuest removed from the reviewers list!

martinfleis commented 1 year ago

@editorialbot add @naeemkh as reviewer

editorialbot commented 1 year ago

@naeemkh added to the reviewers list!

Naeemkh commented 1 year ago

Review checklist for @Naeemkh

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/JeremyGelb/geocmeans?
[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 (@JeremyGelb) 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?

Naeemkh 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:

Naeemkh commented 1 year ago

Thank you for your dedication to this package; I appreciate the effort put into it. One aspect I'd like clarification on is the expectation of reproducibility when setting seed values. As we know, clustering algorithms can yield different results based on initial starting points. However, consistent results are anticipated when beginning from the same state. Could you please confirm whether setting seed values in your package ensures consistent outcomes?

JeremyGelb commented 1 year ago

Dear @Naeemkh ,

indeed, reproductibility is an important issue. Most of the functions in geocmeans have an argument seed that can be set by the user and that will ensure that the results are identical with the same value of seed. See for example the functions CMeans(), GCMeans, SFCMeans, SGFCMeans, select_parameters, and boot_group_validation. Basically, the seed parameter is used internally at the beginning of the execution with a call to the function set.seed. I will edit the documentation to make it clearer.

Naeemkh commented 1 year ago

@JeremyGelb, I appreciate the clarification. Could you also update the website documentation? I had issues running the advanced examples in the vignettes. @martinfleis, I've completed the review and checklist.

martinfleis commented 1 year ago

@Naeemkh Thank you!

Could you also update the website documentation? I had issues running the advanced examples in the vignettes.

This does not block the publication, in your opinion?

Naeemkh commented 1 year ago

@martinfleis, Yes. The issue is resolved: https://github.com/JeremyGelb/geocmeans/issues/7

martinfleis commented 1 year ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a PR)
[x] Check the references in the paper for corrections (e.g. capitalization)
[x] Check that the archive title, author list, version tag, and the license are correct
[x] Set archive DOI with @editorialbot set <DOI here> as archive
[x] Set version with @editorialbot set <version here> as version
[x] Double check rendering of paper with @editorialbot generate pdf
[x] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[x] Recommend acceptance with @editorialbot recommend-accept

martinfleis 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

- 10.4000/cybergeo.36414 is OK
- 10.1016/j.patcog.2006.07.011 is OK
- 10.1016/j.dsp.2012.09.016 is OK
- 10.1007/s00180-018-0791-1 is OK
- 10.2307/622300 is OK
- 10.1080/13658810600665111 is OK
- 10.1111/j.1538-4632.2006.00689.x is OK
- 10.1016/j.cageo.2015.05.019 is OK
- 10.1016/j.patcog.2011.02.009 is OK
- 10.1016/0167-8655(91)90002-4 is OK

MISSING DOIs

- None

INVALID DOIs

- None

martinfleis 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:

martinfleis commented 1 year ago

Thank you, @ljwolf and @Naeemkh for your reviews!

@JeremyGelb please have a look at the checklist of the Additional Author Tasks in the post above.

JeremyGelb commented 1 year ago

Thank you all. I am preparing the new submission to CRAN, but as always I got weird NOTES. I will proceed with the checklist when everything is ready.

This time, I got on debian :

* checking re-building of vignette outputs ... [279s/99s] NOTE
Re-building vignettes had CPU time 2.8 times elapsed time

I have contacted the CRAN team because I could not find online what it means.

JeremyGelb commented 1 year ago

So, I managed to resubmit to CRAN,

Here is the Zenodo DOI : https://doi.org/10.5281/zenodo.8316593

The title, the authors and the ORCIDs are matching.

A release was created on github : https://github.com/JeremyGelb/geocmeans/releases/tag/documentation

martinfleis commented 1 year ago

@JeremyGelb thanks. Tags usually represent a version of each release, e.g. v0.3.4. In you case, the tag is documentation. It is unclear how that is planned to evolve in future. See for example {sf}'s approach to tags. JOSS expectations are not explicit here but the rules implicitly assume that the tag follows the pattern tag==version. Would you mind changing that? I suppose the system would be fine with the documentation tag as well, but it is a bit strange, so if that is not an issue, I'd prefer a standard tag.

JeremyGelb commented 1 year ago

@martinfleis, I just changed the tag of the release and it is now v0.3.4 as requested.

martinfleis commented 1 year ago

@editorialbot set 10.5281/zenodo.8316593 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8316593

martinfleis commented 1 year ago

@editorialbot set v0.3.4 as version

editorialbot commented 1 year ago

Done! version is now v0.3.4

martinfleis commented 1 year ago

@editorialbot generate pdf

openjournals / joss-reviews

[REVIEW]: geocmeans: An R package for spatial fuzzy c-means #5259

Status

Reviewer instructions & questions

Checklists

Review checklist for @ljwolf

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @Naeemkh

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance