editorialbot commented 4 months ago

Submitting author: !--author-handle-->@EFAcar@lrnv<!--end-editor-- Reviewers: @AlexisDerumigny, @mingzehuang Archive: 10.5281/zenodo.13801203

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/afcfb8087e388f2ff802285daadf66c4"><img src="https://joss.theoj.org/papers/afcfb8087e388f2ff802285daadf66c4/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/afcfb8087e388f2ff802285daadf66c4/status.svg)](https://joss.theoj.org/papers/afcfb8087e388f2ff802285daadf66c4)

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

@AlexisDerumigny & @mingzehuang, 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 @lrnv 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 @mingzehuang

📝 Checklist for @AlexisDerumigny

editorialbot commented 4 months 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 4 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (3100.3 files/s, 167245.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               42            196            602           1181
C/C++ Header                    32            120            301            664
XML                              1              0              2            441
Markdown                         4             98              0            283
Rmd                              2             72            260            215
TeX                              2             31              8            148
C++                              4             12              9            134
YAML                             2             11              6             55
CSV                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            90            540           1188           3127
-------------------------------------------------------------------------------

Commit count by author:

    53  mlysy
    18  EFAcar
     6  Elif Fidan Acar
     1  alank2004

editorialbot commented 4 months ago

Paper file info:

📄 Wordcount for paper.md is 1625

✅ The paper includes a Statement of need section

editorialbot commented 4 months ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 4 months ago

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

lrnv commented 4 months ago

👋🏼 @EFAcar, @AlexisDerumigny, @mingzehuang this is the review thread for the paper. All of our communications will happen here from now on.

@AlexisDerumigny, @mingzehuang, as reviewers, 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#6744 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 (@lrnv) if you have any questions/concerns.

editorialbot commented 4 months ago

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

OK DOIs

- 10.1201/9781315370279 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1016/j.ecosta.2019.03.002 is OK
- 10.1111/j.1541-0420.2010.01472.x is OK
- 10.1214/13-EJS866 is OK
- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK

MISSING DOIs

- No DOI given, and none found for title: LocalCop: LocalCop: Local Likelihood Inference for...
- No DOI given, and none found for title: copula: Multivariate Dependence with Copulas
- No DOI given, and none found for title: VineCopula: Statistical Inference of Vine Copulas
- No DOI given, and none found for title: gamCopula: Generalized Additive Models for Bivaria...
- No DOI given, and none found for title: CondCopulas: Estimation and Inference for Conditio...

INVALID DOIs

- None

mingzehuang commented 4 months ago

Review checklist for @mingzehuang

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/mlysy/LocalCop?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@EFAcar) 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?

lrnv commented 4 months ago

👋 @AlexisDerumigny & @mingzehuang How is it going with this review ? If you want/need, I could setup automatic reminders for you on this thread in like 1 week or 2. We usually aim at a 6-to-8 week reviewing time so you still have room ofc

mingzehuang commented 4 months ago

Thank you for your reminder, @lrnv ! It goes smoothly. And I can wrap it up very soon once the author addressed the issues I raised :)

lrnv commented 3 months ago

@AlexisDerumigny gentle bump :)

mingzehuang commented 3 months ago

Hi, @lrnv. I've finished the review, and the author has addressed my concerns. I recommend accepting this paper :)

AlexisDerumigny commented 1 month ago

Review checklist for @AlexisDerumigny

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/mlysy/LocalCop?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@EFAcar) 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?

AlexisDerumigny commented 1 month ago

@AlexisDerumigny gentle bump :)

Thanks for the reminder @lrnv ! I am sorry for being so late, I had some personal problems. Now, the review is nearly completed up to two issues that I have opened.

AlexisDerumigny commented 4 weeks ago

Hi @lrnv, all my comments have been answered and I recommend the paper to be accepted.

lrnv commented 3 weeks ago

@editorialbot generate pdf

editorialbot commented 3 weeks ago

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

lrnv commented 3 weeks ago

@editorialbot check references

lrnv commented 3 weeks ago

@editorialbot check repository

editorialbot commented 3 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (3076.8 files/s, 169465.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               42            198            608           1225
C/C++ Header                    32            120            305            680
XML                              1              0              2            441
Markdown                         4            111              0            296
Rmd                              2             75            261            215
TeX                              2             31              8            148
C++                              4             12              9            134
YAML                             2             11              6             55
CSV                              1              0              0              6
-------------------------------------------------------------------------------
SUM:                            90            558           1199           3200
-------------------------------------------------------------------------------

Commit count by author:

    57  mlysy
    21  EFAcar
     6  Elif Fidan Acar
     1  alank2004

editorialbot commented 3 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1625

✅ The paper includes a Statement of need section

editorialbot commented 3 weeks ago

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

editorialbot commented 3 weeks ago

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

✅ OK DOIs

- 10.1201/9781315370279 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1016/j.ecosta.2019.03.002 is OK
- 10.1111/j.1541-0420.2010.01472.x is OK
- 10.1214/13-EJS866 is OK
- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: LocalCop: LocalCop: Local Likelihood Inference for...
- No DOI given, and none found for title: copula: Multivariate Dependence with Copulas

❌ MISSING DOIs

- 10.32614/cran.package.vinecopula may be a valid DOI for title: VineCopula: Statistical Inference of Vine Copulas
- 10.32614/cran.package.gamcopula may be a valid DOI for title: gamCopula: Generalized Additive Models for Bivaria...
- 10.32614/cran.package.condcopulas may be a valid DOI for title: CondCopulas: Estimation and Inference for Conditio...

❌ INVALID DOIs

- None

lrnv commented 3 weeks ago

@EFAcar congratulations, we are reaching the end of this review. Would you please fix de missing DOI's before we can go to the post-review process ?

EFAcar commented 3 weeks ago

Thank you @lrnv. We've added DOIs for all CRAN packages (including the skipped ones) above.

lrnv commented 3 weeks ago

@editorialbot check references

editorialbot commented 3 weeks ago

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

✅ OK DOIs

- 10.1201/9781315370279 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1016/j.ecosta.2019.03.002 is OK
- 10.1111/j.1541-0420.2010.01472.x is OK
- 10.1214/13-EJS866 is OK
- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: LocalCop: LocalCop: Local Likelihood Inference for...
- No DOI given, and none found for title: copula: Multivariate Dependence with Copulas

❌ MISSING DOIs

- 10.32614/cran.package.vinecopula may be a valid DOI for title: VineCopula: Statistical Inference of Vine Copulas
- 10.32614/cran.package.gamcopula may be a valid DOI for title: gamCopula: Generalized Additive Models for Bivaria...
- 10.32614/cran.package.condcopulas may be a valid DOI for title: CondCopulas: Estimation and Inference for Conditio...

❌ INVALID DOIs

- None

lrnv commented 3 weeks ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
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.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
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 pull request)
[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

lrnv commented 3 weeks ago

@EFAcar Could you take care of your side of the (upper) post-review check list ?

EFAcar commented 1 week ago

@lrnv, @mingzehuang, @AlexisDerumigny thank you for the helpful review comments which have much improved our submission. Please find the post-review check list below:

[x] Double check authors and affiliations (including ORCIDs) Thanks for asking us to double-check these. These have been updated on the paper branch mlysy/joss after the post-review checks began. The most recent manuscript file is vignettes/joss/paper.md on that branch.
[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. The post-review software has been released on CRAN. The version number for the release is 0.0.2.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here. The archive is posted on Zenodo with DOI https://doi.org/10.5281/zenodo.13801203.
[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.

lrnv commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

lrnv commented 1 week ago

@EFAcar Everytthing looks good, except that the Zenodo archive's title and the paper title must be the same, could you change one of them so that they match ?

lrnv commented 1 week ago

@editorialbot set 10.5281/zenodo.13801203 as archive

editorialbot commented 1 week ago

Done! archive is now 10.5281/zenodo.13801203

lrnv commented 1 week ago

@editorialbot set v0.0.2 as version

editorialbot commented 1 week ago

Done! version is now v0.0.2

lrnv commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago

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

✅ OK DOIs

- 10.1201/9781315370279 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1016/j.ecosta.2019.03.002 is OK
- 10.1111/j.1541-0420.2010.01472.x is OK
- 10.1214/13-EJS866 is OK
- 10.32614/CRAN.package.LocalCop is OK
- 10.32614/CRAN.package.copula is OK
- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.32614/CRAN.package.VineCopula is OK
- 10.32614/CRAN.package.gamCopula is OK
- 10.32614/CRAN.package.CondCopulas is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

EFAcar commented 1 week ago

@EFAcar Everytthing looks good, except that the Zenodo archive's title and the paper title must be the same, could you change one of them so that they match ?

@lrnv the title for the Zenodo archive is now corrected.

lrnv commented 1 week ago

@editorialbot recommend-accept

editorialbot commented 1 week ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 week ago

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

✅ OK DOIs

- 10.1201/9781315370279 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1016/j.ecosta.2019.03.002 is OK
- 10.1111/j.1541-0420.2010.01472.x is OK
- 10.1214/13-EJS866 is OK
- 10.32614/CRAN.package.LocalCop is OK
- 10.32614/CRAN.package.copula is OK
- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.32614/CRAN.package.VineCopula is OK
- 10.32614/CRAN.package.gamCopula is OK
- 10.32614/CRAN.package.CondCopulas is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

editorialbot commented 1 week ago

:warning: Error preparing paper acceptance. The generated XML metadata file is invalid.

No declaration for attribute displaystyle of element mfrac
No declaration for attribute displaystyle of element mfrac

lrnv commented 1 week ago

@EFAcar can you fix this?

EFAcar commented 1 week ago

@lrnv based on this review the error code seems to be due to using displaymode with \dfrac. We now changed these to \frac. Hope this will fix the issue.

lrnv commented 1 week ago

@EFAcar ha yes it is true that you cant re-launch the process yourself. Let me check if it did it

lrnv commented 1 week ago

@editorialbot recommend-accept

editorialbot commented 1 week ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 week ago

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

✅ OK DOIs

- 10.1201/9781315370279 is OK
- 10.18637/jss.v070.i05 is OK
- 10.1016/j.ecosta.2019.03.002 is OK
- 10.1111/j.1541-0420.2010.01472.x is OK
- 10.1214/13-EJS866 is OK
- 10.32614/CRAN.package.LocalCop is OK
- 10.32614/CRAN.package.copula is OK
- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.32614/CRAN.package.VineCopula is OK
- 10.32614/CRAN.package.gamCopula is OK
- 10.32614/CRAN.package.CondCopulas is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

openjournals / joss-reviews

[REVIEW]: LocalCop: An R package for local likelihood inference for conditional copulas #6744

Status

Reviewer instructions & questions

Checklists

Review checklist for @mingzehuang

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @AlexisDerumigny

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