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[REVIEW]: VineCopulas: an open-source Python package for vine copula modelling #6728

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editorialbot opened this issue May 7, 2024 · 18 comments
Open

[REVIEW]: VineCopulas: an open-source Python package for vine copula modelling #6728

editorialbot opened this issue May 7, 2024 · 18 comments
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Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented May 7, 2024 •
edited

Submitting author: @judithclaassen (Judith Claassen)
Repository: https://github.com/VU-IVM/VineCopulas
Branch with paper.md (empty if default branch):
Version: v0.2.5
Editor: @ymzayek
Reviewers: @haozcbnu, @couasnonanais
Archive: Pending

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/5118d62bcc8a3621ebdd2955f8e88405"><img src="https://joss.theoj.org/papers/5118d62bcc8a3621ebdd2955f8e88405/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/5118d62bcc8a3621ebdd2955f8e88405/status.svg)](https://joss.theoj.org/papers/5118d62bcc8a3621ebdd2955f8e88405)

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

@haozcbnu & @couasnonanais, 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 @ymzayek 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 @haozcbnu

📝 Checklist for @couasnonanais
@editorialbot editorialbot added Python review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning labels May 7, 2024
@editorialbot editorialbot mentioned this issue May 7, 2024
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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

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (336.7 files/s, 144225.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           7            718            556           5284
CSV                              2              0              0           1408
Jupyter Notebook                 2              0           1742            264
Markdown                         5            103              0            262
TeX                              1             17              0            127
YAML                             6             18             20            119
TOML                             1              5              0             37
reStructuredText                 1             11              7             11
-------------------------------------------------------------------------------
SUM:                            25            872           2325           7512
-------------------------------------------------------------------------------

Commit count by author:

   109	Claassen
    52	Judith Claassen
     9	Jäger
     6	Elco Koks
     1	Koks

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Paper file info:

📄 Wordcount for paper.md is 1016

✅ The paper includes a Statement of need section

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License info:

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

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

OK DOIs

- 10.3389/fnins.2022.910122 is OK
- 10.1201/b17116 is OK
- 10.1146/annurev-statistics-040220-101153 is OK
- 10.5281/ZENODO.10435751 is OK
- 10.1214/aos/1031689016 is OK
- 10.1201/9780367803896 is OK
- 10.5194/nhess-23-2251-2023 is OK
- 10.5194/hess-21-2701-2017 is OK

MISSING DOIs

- 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: CDVineCopulaConditional: Sampling from Conditional...
- No DOI given, and none found for title: copulas: Create tabular synthetic data using copul...
- No DOI given, and none found for title: Monte Carlo simulation of vine dependent random va...

INVALID DOIs

- None

@ymzayek
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ymzayek commented May 7, 2024

@haozcbnu and @couasnonanais

Dear reviewers, you can start your review by creating your tasklist with the following command:

@editorialbot generate my checklist

In that list, there are several tasks. Whenever you perform a task, you can check on the corresponding checkbox. You can also reference the JOSS reviewer guidelines which is linked in first comment in this thread. Since the review process of JOSS is interactive, you can always interact with the author, the other reviewers, and the editor during the process. You can open issues and pull requests in the target repo. Please mention the url of this page in there so that we can keep tracking what is going on.

Thank you in advance.

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

@haozcbnu
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haozcbnu commented May 14, 2024 •
edited

Review checklist for @haozcbnu

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/VU-IVM/VineCopulas?
  • 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 (@judithclaassen) 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?

@ymzayek
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ymzayek commented May 16, 2024

@couasnonanais let me know if you are able to get started on this soon. Thanks!

@couasnonanais
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couasnonanais commented May 16, 2024 •
edited

Review checklist for @couasnonanais

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

General checks

  • Repository: Is the source code for this software available at the https://github.com/VU-IVM/VineCopulas?
  • 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 (@judithclaassen) 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?

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


# List all available commands
@editorialbot commands

# Get a list of all editors's GitHub handles
@editorialbot list editors

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

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

# Run checks and provide information on the repository and the paper file
@editorialbot check repository

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

# 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

@haozcbnu
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haozcbnu commented May 17, 2024 •
edited

Here are several comments/suggestions.

Lines 9-10: Here some references can be given to introduce the basic concept of Copula.

Lines 15-16: please check the punctuation mark.

Lines 19-22: Here the concept of the "curse of dimensionality " can be introduced to demonstrate the challenge in multivariate dependence modeling.

Captions of Figure 1: D) What do you mean by " As not every vine copula structure is suitable to generate conditional samples of every variable"? E) Drawing conditional samples of the variable 1 given specific values of variables 2 and 3? This needs to be clear.

Lines 59-61: To emphasize the usefulness of this package, the authors can highlight the large number of variables or hazards (>2) in the multi-hazard phenomenon.

@ymzayek
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ymzayek commented May 28, 2024

Hello @couasnonanais do you have an update on your review?

@ymzayek
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ymzayek commented May 28, 2024

Here are several comments/suggestions.

Lines 9-10: Here some references can be given to introduce the basic concept of Copula.

Lines 15-16: please check the punctuation mark.

Lines 19-22: Here the concept of the "curse of dimensionality " can be introduced to demonstrate the challenge in multivariate dependence modeling.

Captions of Figure 1: D) What do you mean by " As not every vine copula structure is suitable to generate conditional samples of every variable"? E) Drawing conditional samples of the variable 1 given specific values of variables 2 and 3? This needs to be clear.

Lines 59-61: To emphasize the usefulness of this package, the authors can highlight the large number of variables or hazards (>2) in the multi-hazard phenomenon.

@haozcbnu can you clarify the status regarding these comments? Any updates there?

@judithclaassen
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Here are several comments/suggestions.
Lines 9-10: Here some references can be given to introduce the basic concept of Copula.
Lines 15-16: please check the punctuation mark.
Lines 19-22: Here the concept of the "curse of dimensionality " can be introduced to demonstrate the challenge in multivariate dependence modeling.
Captions of Figure 1: D) What do you mean by " As not every vine copula structure is suitable to generate conditional samples of every variable"? E) Drawing conditional samples of the variable 1 given specific values of variables 2 and 3? This needs to be clear.
Lines 59-61: To emphasize the usefulness of this package, the authors can highlight the large number of variables or hazards (>2) in the multi-hazard phenomenon.

@haozcbnu can you clarify the status regarding these comments? Any updates there?

@haozcbnu Thank you so much for providing us with your review. @ymzayek I would prefer to incorporate the suggestions after having received @couasnonanais review as well, if possible.

@couasnonanais
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couasnonanais commented Jun 4, 2024 via email

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ymzayek commented Jun 11, 2024

@couasnonanais let me know if you will have time to finish your review soon. If for whatever reason it is not possible for you that is ok but then it might be necessary to look for a new reviewer. Let me know if I can be of any help. Thanks!

@couasnonanais
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couasnonanais commented Jun 13, 2024 via email

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