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

editorialbot · 2024-05-13T08:34:39Z

Submitting author: @EFAcar (Elif Acar)
Repository: https://github.com/mlysy/LocalCop
Branch with paper.md (empty if default branch): joss
Version: v0.0.2
Editor: @lrnv
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

The text was updated successfully, but these errors were encountered:

editorialbot · 2024-05-13T08:34:42Z

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

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editorialbot · 2024-05-13T08:35:16Z

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 · 2024-05-13T08:35:20Z

Paper file info:

📄 Wordcount for paper.md is 1625

✅ The paper includes a Statement of need section

editorialbot · 2024-05-13T08:35:23Z

License info:

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

editorialbot · 2024-05-13T08:36:07Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

lrnv · 2024-05-13T08:36:22Z

👋🏼 @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 · 2024-05-13T08:37:45Z

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 · 2024-05-17T05:24:57Z

Review checklist for @mingzehuang

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/mlysy/LocalCop?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
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?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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 · 2024-05-27T20:32:21Z

👋 @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 · 2024-05-29T20:10:02Z

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 · 2024-06-11T07:24:08Z

@AlexisDerumigny gentle bump :)

mingzehuang · 2024-06-25T07:22:12Z

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

AlexisDerumigny · 2024-08-05T15:38:28Z

Review checklist for @AlexisDerumigny

Conflict of interest

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

I confirm that I read and will adhere to the JOSS code of conduct.

General checks

Repository: Is the source code for this software available at the https://github.com/mlysy/LocalCop?
License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
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?
Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
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.
Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
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

Installation: Does installation proceed as outlined in the documentation?
Functionality: Have the functional claims of the software been confirmed?
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

A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
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

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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?
State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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 · 2024-08-05T16:18:50Z

@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 · 2024-09-04T07:26:29Z

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

lrnv · 2024-09-09T07:33:03Z

@editorialbot generate pdf

editorialbot · 2024-09-09T07:34:22Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

lrnv · 2024-09-09T07:38:51Z

@editorialbot check references

lrnv · 2024-09-09T07:38:57Z

@editorialbot check repository

lrnv · 2024-09-20T15:58:05Z

@editorialbot recommend-accept

editorialbot · 2024-09-20T15:58:08Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-09-20T15:58:28Z

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 · 2024-09-20T15:59:58Z

⚠️ 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 · 2024-09-22T10:46:07Z

@EFAcar can you fix this?

EFAcar · 2024-09-23T01:53:53Z

@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 · 2024-09-23T06:38:31Z

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

lrnv · 2024-09-23T06:38:33Z

@editorialbot recommend-accept

editorialbot · 2024-09-23T06:38:35Z

Attempting dry run of processing paper acceptance...

editorialbot · 2024-09-23T06:38:51Z

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 · 2024-09-23T06:40:26Z

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5899, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

crvernon · 2024-09-23T18:05:52Z

editorialbot · 2024-09-23T18:07:12Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

crvernon · 2024-09-24T14:03:43Z

@EFAcar - this is looking good. I just need you to address the following minor items before I accept for publication:

LINE 85: "LocalCop:" is repeated in the reference
LINE 91: The "a" in "archimedean" should be capitalized. You can maintain capitalization in your references by using curly brackets around the characters you wish to maintain formatting for.

No need to conduct another release.

Let me know once these have been corrected and I will accept this for publication.

EFAcar · 2024-09-24T20:37:02Z

@crvernon Thanks very much for catching these. They have now been fixed in this PR.

crvernon · 2024-09-25T11:48:53Z

@editorialbot generate pdf

editorialbot · 2024-09-25T11:50:09Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

crvernon · 2024-09-25T11:53:20Z

@editorialbot accept

editorialbot · 2024-09-25T11:53:22Z

Doing it live! Attempting automated processing of paper acceptance...

lrnv · 2024-09-25T11:54:58Z

GG @EFAcar !!

editorialbot · 2024-09-25T12:00:02Z

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Acar
  given-names: Elif Fidan
  orcid: "https://orcid.org/0000-0003-2908-7691"
- family-names: Lysy
  given-names: Martin
  orcid: "https://orcid.org/0000-0001-9974-1121"
- family-names: Kuchinsky
  given-names: Alan
doi: 10.5281/zenodo.13801203
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Acar
    given-names: Elif Fidan
    orcid: "https://orcid.org/0000-0003-2908-7691"
  - family-names: Lysy
    given-names: Martin
    orcid: "https://orcid.org/0000-0001-9974-1121"
  - family-names: Kuchinsky
    given-names: Alan
  date-published: 2024-09-25
  doi: 10.21105/joss.06744
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6744
  title: "LocalCop: An R package for local likelihood inference for
    conditional copulas"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06744"
  volume: 9
title: "LocalCop: An R package for local likelihood inference for
  conditional copulas"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

editorialbot · 2024-09-25T12:00:06Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-09-25T12:00:06Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06744 joss-papers#5909
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06744
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

crvernon · 2024-09-25T12:04:22Z

🥳 Congratulations on your new publication @EFAcar! Many thanks to @lrnv for editing and @AlexisDerumigny and @mingzehuang for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

editorialbot · 2024-09-25T12:04:24Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.06744/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06744/status.svg
   :target: https://doi.org/10.21105/joss.06744

This is how it will look in your documentation:

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EFAcar · 2024-09-25T18:53:39Z

@crvernon, @lrnv, @mingzehuang, @AlexisDerumigny thank you again for a very constructive review process!

editorialbot added C++ R review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels May 13, 2024

editorialbot assigned lrnv May 13, 2024

editorialbot mentioned this issue May 13, 2024

[PRE REVIEW]: LocalCop: An R package for local likelihood inference for conditional copulas #6560

Closed

mingzehuang mentioned this issue May 17, 2024

Community Guideline mlysy/LocalCop#7

Closed

mingzehuang mentioned this issue May 27, 2024

Documentation Style mlysy/LocalCop#10

Closed

This was referenced Aug 5, 2024

Documentation mismatch for ConvertPar mlysy/LocalCop#15

Closed

Add link to TMB package in the README mlysy/LocalCop#16

Closed

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Sep 23, 2024

editorialbot added accepted published Papers published in JOSS labels Sep 25, 2024

crvernon closed this as completed Sep 25, 2024

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

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

Comments

editorialbot commented May 13, 2024 • edited Loading

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Reviewer instructions & questions

Checklists

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mingzehuang commented May 17, 2024 • edited by lrnv Loading

Review checklist for @mingzehuang

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

lrnv commented May 27, 2024

mingzehuang commented May 29, 2024

lrnv commented Jun 11, 2024

mingzehuang commented Jun 25, 2024

AlexisDerumigny commented Aug 5, 2024 • edited Loading

Review checklist for @AlexisDerumigny

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

AlexisDerumigny commented Aug 5, 2024

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EFAcar commented Sep 25, 2024

editorialbot commented May 13, 2024 •

edited

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edited by lrnv

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