[REVIEW]: spINAR: An R Package for Semiparametric and Parametric Estimation and Bootstrapping of Integer-Valued Autoregressive (INAR) Models
Closed this issue · 70 comments
Submitting author: @MFaymon (Maxime Faymonville)
Repository: https://github.com/MFaymon/spINAR
Branch with paper.md (empty if default branch):
Version: v0.2.0
Editor: @crsl4
Reviewers: @ManuelStapper, @SaranjeetKaur, @wittenberg
Archive: 10.5281/zenodo.10944202
Status
Status badge code:
HTML: <a href="https://joss.theoj.org/papers/6fcfcc77635fdd18153b35d5986fe2aa"><img src="https://joss.theoj.org/papers/6fcfcc77635fdd18153b35d5986fe2aa/status.svg"></a>
Markdown: [](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
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
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
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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
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SUM: 32 177 364 1979
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gitinspector failed to run statistical information for the repository
Wordcount for paper.md is 708
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
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?
Opened an issue over at the package Repo (HERE) for comments and questions.
I completed the checklist, the issues I opened have been addressed.
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?
Hello @SaranjeetKaur just checking in! How are things going on your end for this review? :)
Hey @SaranjeetKaur, @crsl4, just a kindly reminder that we are still waiting for the second review :)
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.
Hi @SaranjeetKaur I am happy to wait for you to complete this review. How much time do you think you would need?
I am occupied until mid October.
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 !
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.
Hello @wittenberg, would you be interested in reviewing this manuscript? Thanks for considering it!
Hi @crsl4, I can do the review for this manuscript.
Thank you Philipp!
@editorialbot add @wittenberg as reviewer
@wittenberg added to the reviewers list!
@editorialbot please provide Review checklist
I'm sorry human, I don't understand that. You can see what commands I support by typing:
@editorialbot commands
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?
Hello @wittenberg @SaranjeetKaur, any updates on reviews? Thanks!
Hi @crsl4,
Sorry, I don't have the time to pick up on this!
Hello @wittenberg any updates on your review?
Tagging also @SaranjeetKaur in case your plate is clearer now and could finish the review 🤞.
I have created an issue at the package repository (MFaymon/spINAR#5) to encourage discussion and feedback.
Thanks a lot for the review @wittenberg! I adressed all the suggestions for improvement, see (MFaymon/spINAR#5), @crsl4.
@MFaymon Thank you for considering and implementing the suggestions. @crsl4 and @editorialbot, all the issues have been addressed.
@crsl4 – I think this submission is good to move forward to the last checks before recommending acceptance here?
Yes, that's true! I'll do the last checks.
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 referencesand ask author(s) to update as needed - Recommend acceptance with
@editorialbot recommend-accept
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 :)
@crsl4 just a gentle reminder that everything is completed here from the author's side
Yes, sorry for the slowness! I have a difficult deadline for May 3, but I will do this immediately after that.
@editorialbot generate pdf
@editorialbot check references
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
- No DOI given, and none found for title: First-order integer-valued autoregressive (INAR(1)...
- No DOI given, and none found for title: Efficient estimation of auto-regression parameters...
- No DOI given, and none found for title: The integer valued autoregressive (INAR(p)) model
- No DOI given, and none found for title: Conditional maximum-likelihood estimates for INAR(...
- 10.1111/j.1467-9892.2012.00809.x may be a valid DOI for title: First-order integer valued AR processes with zero ...
- 10.3150/18-bej1057 may be a valid DOI for title: Bootstrapping INAR Models
- No DOI given, and none found for title: Some simple models for discrete variate time serie...
- 10.1016/j.ijforecast.2004.11.001 may be a valid DOI for title: Bayesian predictions of low count time series
- 10.1214/aop/1176994950 may be a valid DOI for title: Discrete analogues of self-decomposability and sta...
- 10.1002/(sici)1099-095x(199907/08)10:4<395::aid-env364>3.3.co;2-d may be a valid DOI for title: Integer valued autoregressive models for tipping b...
- No DOI given, and none found for title: An Introduction to Discrete-Valued Time Series
- No DOI given, and none found for title: Categorical Times Series Analysis and Applications...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: ZINARp: Simulate INAR/ZINAR(p) Models and Estimate...
INVALID DOIs
- None
@editorialbot set v0.2.0 as version
Done! version is now v0.2.0
@editorialbot set 10.5281/zenodo.10944202 as archive
👋 @MFaymon - I am the AEiC for the track this submission in on. I am going to team with @crsl4 to move this one forward as you are very close to publication!
The following are a few minor things for you to address before we can move forward:
- The title and authors of your Zenodo record (https://zenodo.org/records/10944202) should match the title from your paper. Please endure the authors also appear in the same order if they do not already. Please also change the license specified in your Zenodo archive from CC 4.0 to what is in your repo for your software (GPL-3.0). You can do all of this without having to make another release...just edit the metadata for the record and you should be good.
- Please check the following references for potential DOIs as rendered from #5386 (comment):
- 10.1111/j.1467-9892.2012.00809.x may be a valid DOI for title: First-order integer valued AR processes with zero ...
- 10.3150/18-bej1057 may be a valid DOI for title: Bootstrapping INAR Models
- 10.1016/j.ijforecast.2004.11.001 may be a valid DOI for title: Bayesian predictions of low count time series
- 10.1214/aop/1176994950 may be a valid DOI for title: Discrete analogues of self-decomposability and sta...
There is no reason to make any new releases when incorporating any changes above since these are all in reference to the paper or archive.
Thanks so much and I look forward to hearing back from you soon so we can get all of your hard work in the books!
Done! archive is now 10.5281/zenodo.10944202
Hi @crvernon, thanks for your contribution! I added/changed everything you requested. See the changes in Zenodo and commit 73348aa.
@editorialbot generate pdf
@editorialbot check references
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1111/j.1467-9892.2012.00809.x is OK
- 10.3150/18-BEJ1057 is OK
- 10.1137/141000671 is OK
- 10.1007/s10260-022-00655-0 is OK
- 10.5281/zenodo.7488440 is OK
- 10.1016/j.ijforecast.2004.11.001 is OK
- 10.1214/aop/1176994950 is OK
- 10.18637/jss.v082.i05 is OK
MISSING DOIs
- No DOI given, and none found for title: First-order integer-valued autoregressive (INAR(1)...
- No DOI given, and none found for title: Efficient estimation of auto-regression parameters...
- No DOI given, and none found for title: The integer valued autoregressive (INAR(p)) model
- No DOI given, and none found for title: Conditional maximum-likelihood estimates for INAR(...
- No DOI given, and none found for title: Some simple models for discrete variate time serie...
- 10.1002/(sici)1099-095x(199907/08)10:4<395::aid-env364>3.3.co;2-d may be a valid DOI for title: Integer valued autoregressive models for tipping b...
- No DOI given, and none found for title: An Introduction to Discrete-Valued Time Series
- No DOI given, and none found for title: Categorical Times Series Analysis and Applications...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: ZINARp: Simulate INAR/ZINAR(p) Models and Estimate...
INVALID DOIs
- None
@editorialbot recommend-accept
✅ This is looking good @MFaymon! I am going to move forward with the acceptance process.
🙌 Thanks so much to @crsl4 for editing and @ManuelStapper and @wittenberg for a constructive review!
Attempting dry run of processing paper acceptance...
👋 @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#5315, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):
OK DOIs
- 10.1111/j.1467-9892.2012.00809.x is OK
- 10.3150/18-BEJ1057 is OK
- 10.1137/141000671 is OK
- 10.1007/s10260-022-00655-0 is OK
- 10.5281/zenodo.7488440 is OK
- 10.1016/j.ijforecast.2004.11.001 is OK
- 10.1214/aop/1176994950 is OK
- 10.18637/jss.v082.i05 is OK
MISSING DOIs
- No DOI given, and none found for title: First-order integer-valued autoregressive (INAR(1)...
- No DOI given, and none found for title: Efficient estimation of auto-regression parameters...
- No DOI given, and none found for title: The integer valued autoregressive (INAR(p)) model
- No DOI given, and none found for title: Conditional maximum-likelihood estimates for INAR(...
- No DOI given, and none found for title: Some simple models for discrete variate time serie...
- 10.1002/(sici)1099-095x(199907/08)10:4<395::aid-env364>3.3.co;2-d may be a valid DOI for title: Integer valued autoregressive models for tipping b...
- No DOI given, and none found for title: An Introduction to Discrete-Valued Time Series
- No DOI given, and none found for title: Categorical Times Series Analysis and Applications...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: ZINARp: Simulate INAR/ZINAR(p) Models and Estimate...
INVALID DOIs
- None
I checked the proof. Everything looks good from my side :)
@editorialbot accept
Doing it live! Attempting automated processing of paper acceptance...
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: Faymonville
given-names: Maxime
- family-names: Riffo
given-names: Javiera
- family-names: Rieger
given-names: Jonas
- family-names: Jentsch
given-names: Carsten
doi: 10.5281/zenodo.10944202
message: If you use this software, please cite our article in the
Journal of Open Source Software.
preferred-citation:
authors:
- family-names: Faymonville
given-names: Maxime
- family-names: Riffo
given-names: Javiera
- family-names: Rieger
given-names: Jonas
- family-names: Jentsch
given-names: Carsten
date-published: 2024-05-08
doi: 10.21105/joss.05386
issn: 2475-9066
issue: 97
journal: Journal of Open Source Software
publisher:
name: Open Journals
start: 5386
title: "spINAR: An R Package for Semiparametric and Parametric
Estimation and Bootstrapping of Integer-Valued Autoregressive (INAR)
Models"
type: article
url: "https://joss.theoj.org/papers/10.21105/joss.05386"
volume: 9
title: "spINAR: An R Package for Semiparametric and Parametric
Estimation and Bootstrapping of Integer-Valued Autoregressive (INAR)
Models"
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.
🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘
🚨🚨🚨 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 👉 openjournals/joss-papers#5318
- Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05386
- If everything looks good, then close this review issue.
- Party like you just published a paper! 🎉🌈🦄💃👻🤘
Any issues? Notify your editorial technical team...
Congratulations on your new publication @MFaymon! Many thanks to @crsl4 for editing and @ManuelStapper and @wittenberg for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉
If you would like to include a link to your paper from your README use the following code snippets:
Markdown:
[](https://doi.org/10.21105/joss.05386)
HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.05386">
<img src="https://joss.theoj.org/papers/10.21105/joss.05386/status.svg" alt="DOI badge" >
</a>
reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.05386/status.svg
:target: https://doi.org/10.21105/joss.05386
This is how it will look in your documentation:
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