[REVIEW]: spINAR: An R Package for Semiparametric and Parametric Estimation and Bootstrapping of Integer-Valued Autoregressive (INAR) Models

[editorialbot]

Submitting author: @MFaymon (Maxime Faymonville)
Repository: https://github.com/MFaymon/spINAR
Branch with paper.md (empty if default branch):
Version: v0.1.0
Editor: @crsl4
Reviewers: @ManuelStapper, @SaranjeetKaur, @wittenberg
Archive: Pending

Status

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Markdown: [![status](https://joss.theoj.org/papers/6fcfcc77635fdd18153b35d5986fe2aa/status.svg)](https://joss.theoj.org/papers/6fcfcc77635fdd18153b35d5986fe2aa)

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

@ManuelStapper & @SaranjeetKaur, 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 @crsl4 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 @ManuelStapper

📝 Checklist for @SaranjeetKaur

📝 Checklist for @wittenberg

[editorialbot]

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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.02 s (1630.1 files/s, 128369.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               23             96            354           1206
XML                              1              0              2            441
Markdown                         3             52              0            151
TeX                              1             11              0             99
YAML                             3             17              8             80
Bourne Shell                     1              1              0              2
-------------------------------------------------------------------------------
SUM:                            32            177            364           1979
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 708

[editorialbot]

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

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1007/s10260-022-00655-0 is OK
- 10.5281/zenodo.7488440 is OK
- 10.18637/jss.v082.i05 is OK

MISSING DOIs

- 10.3150/18-bej1057 may be a valid DOI for title: Bootstrapping INAR Models
- 10.1111/j.1752-1688.1985.tb05379.x may be a valid DOI for title: Some simple models for discrete variate time series
- 10.1214/aop/1176994950 may be a valid DOI for title: Discrete analogues of self-decomposability and stability

INVALID DOIs

- None

[ManuelStapper]

Review checklist for @ManuelStapper

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/MFaymon/spINAR?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@MFaymon) 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?

[ManuelStapper]

Opened an issue over at the package Repo (HERE) for comments and questions.

[editorialbot]

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

[ManuelStapper]

I completed the checklist, the issues I opened have been addressed.

[SaranjeetKaur]

Review checklist for @SaranjeetKaur

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/MFaymon/spINAR?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@MFaymon) 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?

[editorialbot]

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

[crsl4]

Hello @SaranjeetKaur just checking in! How are things going on your end for this review? :)

[MFaymon]

Hey @SaranjeetKaur, @crsl4, just a kindly reminder that we are still waiting for the second review :)

[SaranjeetKaur]

Hi Folks!
As much as I want to do this, I have a very tight schedule currently. Hence, I would request you to relieve me from this.

[crsl4]

Hi @SaranjeetKaur I am happy to wait for you to complete this review. How much time do you think you would need?

[SaranjeetKaur]

I am occupied until mid October.

[crsl4]

It is so hard to find reviewers, so let's do this! I will try to find a reviewer to replace you, but if unsuccessful, we'll welcome your review in mid-October. Thanks @SaranjeetKaur !

[crsl4]

@MFaymon Please share any recommendations of reviewers that you might have. Thanks!

[MFaymon]

I suggest Dr. Philipp Wittenberg from Helmut-Schmidt-University Hamburg as reviewer. Part of his research deals with autoregressive counts. I suppose that @wittenberg is his GitHub profile.

[crsl4]

Hello @wittenberg, would you be interested in reviewing this manuscript? Thanks for considering it!

[wittenberg]

Hi @crsl4, I can do the review for this manuscript.

[crsl4]

Thank you Philipp!

[crsl4]

@editorialbot add @wittenberg as reviewer

[editorialbot]

@wittenberg added to the reviewers list!

[wittenberg]

@editorialbot please provide Review checklist

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[wittenberg]

Review checklist for @wittenberg

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/MFaymon/spINAR?
• 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 (@MFaymon) 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?

[crsl4]

Hello @wittenberg @SaranjeetKaur, any updates on reviews? Thanks!

[SaranjeetKaur]

Hi @crsl4,

Sorry, I don't have the time to pick up on this!

[crsl4]

Hello @wittenberg any updates on your review?

[crsl4]

Tagging also @SaranjeetKaur in case your plate is clearer now and could finish the review 🤞.

[wittenberg]

I have created an issue at the package repository (MFaymon/spINAR#5) to encourage discussion and feedback.

[crsl4]

thank you! @MFaymon can you take a look?

[MFaymon]

Thanks a lot for the review @wittenberg! I adressed all the suggestions for improvement, see (MFaymon/spINAR#5), @crsl4.

[wittenberg]

@MFaymon Thank you for considering and implementing the suggestions. @crsl4 and @editorialbot, all the issues have been addressed.

[MFaymon]

@crsl4 Does anything else need to be done from my side?

[arfon]

@crsl4 – I think this submission is good to move forward to the last checks before recommending acceptance here?

[crsl4]

Yes, that's true! I'll do the last checks.

[crsl4]

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

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

[crsl4]

@MFaymon please go over the authors' tasks, and I will do the editor's tasks.

[MFaymon]

Version number of latest submission to CRAN: v0.2.0
DOI of latest Zenodo release: 10.5281/zenodo.10944202

The latest CRAN release is not published yet but submitted and on it's way. We also checked the other author's tasks, so there should be nothing left to do from our side :)

[MFaymon]

Now, the latest CRAN release has been published, @crsl4 .

[JonasRieger]

@crsl4 just a gentle reminder that everything is completed here from the author's side

[crsl4]

Yes, sorry for the slowness! I have a difficult deadline for May 3, but I will do this immediately after that.