[REVIEW]: piar: Price Index Aggregation in R

[editorialbot]

Submitting author: @marberts (Steve Martin)
Repository: https://github.com/marberts/piar
Branch with paper.md (empty if default branch): joss
Version: 0.8.1
Editor: @crvernon
Reviewers: @schneiderpy, @realxinzhao
Archive: 10.5281/zenodo.13323298

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/6c0612164db8d119d12b8e3283fe9acb/status.svg)](https://joss.theoj.org/papers/6c0612164db8d119d12b8e3283fe9acb)

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

@schneiderpy & @arne-henningsen, 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 @crvernon 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 @schneiderpy

📝 Checklist for @realxinzhao

[editorialbot]

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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 1.90  T=0.03 s (2350.9 files/s, 227432.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               57            490           1605           3033
Markdown                         5            169              0            450
Rmd                              2            200            237            225
YAML                             5             36             12            192
TeX                              1             14              0            109
-------------------------------------------------------------------------------
SUM:                            70            909           1854           4009
-------------------------------------------------------------------------------

Commit count by author:

   219	Steve Martin
    69	marberts

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1183

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: Other (Check here for OSI approval)

[editorialbot]

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

[crvernon]

👋 @marberts, @schneiderpy, and @arne-henningsen - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also 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 #6781 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

[editorialbot]

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

OK DOIs

- 10.1017/CBO9780511720758 is OK
- 10.5089/9781484354841.069 is OK
- 10.5089/9781589063044.069 is OK
- 10.32614/RJ-2021-038 is OK
- 10.5281/zenodo.10110159 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Chain Indices: A Study in Price Index Theory
- No DOI given, and none found for title: IndexNumR: Index Number Calculation
- No DOI given, and none found for title: cansim: Accessing Statistics Canada Data Table and...
- No DOI given, and none found for title: cpi
- No DOI given, and none found for title: micEconIndex: Price and Quantity Indices
- No DOI given, and none found for title: hpiR: House Price Indexes
- No DOI given, and none found for title: PriceIndices: Calculating Bilateral and Multilater...
- No DOI given, and none found for title: Technical Guide for the For-hire Motor Carrier Fre...
- No DOI given, and none found for title: Technical Guide for the Couriers and Messengers Se...

INVALID DOIs

- None

[marberts]

Thanks @crvernon.

Thanks @schneiderpy and @arne-henningsen for agreeing to review. I'm looking forward to your comments.

[schneiderpy]

Review checklist for @schneiderpy

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/marberts/piar?
• 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 (@marberts) 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?

[marberts]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1017/CBO9780511720758 is OK
- 10.5089/9781484354841.069 is OK
- 10.5089/9781589063044.069 is OK
- 10.32614/RJ-2021-038 is OK
- 10.5281/zenodo.10110159 is OK

MISSING DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Chain Indices: A Study in Price Index Theory
- No DOI given, and none found for title: IndexNumR: Index Number Calculation
- No DOI given, and none found for title: cansim: Accessing Statistics Canada Data Table and...
- No DOI given, and none found for title: cpi
- No DOI given, and none found for title: micEconIndex: Price and Quantity Indices
- No DOI given, and none found for title: hpiR: House Price Indexes
- No DOI given, and none found for title: PriceIndices: Calculating Bilateral and Multilater...
- No DOI given, and none found for title: Technical Guide for the For-hire Motor Carrier Fre...
- No DOI given, and none found for title: Technical Guide for the Couriers and Messengers Se...

INVALID DOIs

- None

[marberts]

@editorialbot generate pdf

[editorialbot]

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

[marberts]

Updated the paper in 3fc76e7 to incorporate @schneiderpy's suggestions in marberts/piar#6.

[crvernon]

👋 @marberts, @schneiderpy, and @arne-henningsen - it looks like you are making good progress. Could you each provide a short update to how things are going here in this thread? Thanks!

[marberts]

@crvernon Here's a short update from me.

I've incorporated several suggestions from @schneiderpy:

• Phrasing and typos marberts/piar#6: corrected some typos and an incorrect reference, and made a couple parts of the paper clearer.
• Summery/Statement of need marberts/piar#8: made the target audience for the package clearer in the paper and README.md.
• Community guidelines marberts/piar#9: added CONTRIBUTING.md to the repo.

A few ideas/suggestions came up in marberts/piar#6. Some of these need more thought (i.e., changing the default behavior of argument matching), but there's good suggestions in here to make the example in the paper a bit clearer.

[schneiderpy]

👋 @marberts, @schneiderpy, and @arne-henningsen - it looks like you are making good progress. Could you each provide a short update to how things are going here in this thread? Thanks!

@crvernon I have almost done ..
From my point of view Unexpected function results seems to be the main issue so far

[marberts]

@editorialbot generate pdf

The code snippets in the example have been re-written to address the comments in marberts/piar#7.

[crvernon]

👋 @marberts - we are almost there!

I only need one change in the paper:

• LINE 141: The "c" in "canada" should be capitalized. This can be done in the bib file by using curly brackets around the characters you wish to maintain the formatting of.

Next is just setting up the archive for your new release.

We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

• Conduct a GitHub release of the current reviewed version of the software and archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository). Please ensure that the software archive uses the same license as the license you have posted on GitHub.

• Check the archival deposit (e.g., in Zenodo) to ensure it has the correct metadata. This includes the title (should match the paper title exactly) and author list (make sure the list is correct and ordered the same as the paper). You may also add the authors' ORCID.

• Please respond with the DOI of the archived version here along with the version number

I can then move forward with accepting the submission.

[marberts]

Thanks, @crvernon.

• Thanks for catching the typo in the reference list. I've corrected the .bib file.
• The reviewed version is released on GitHub. I bumped the version to 0.8.1 to reflect the changes from the review.
• The released version is archived on Zenodo: https://doi.org/10.5281/zenodo.13323298. The title and author list matches the paper, and the license is the same what's on GitHub.

[marberts]

@crvernon I forgot to add that the released/archived version (0.8.1) is on the main branch, along with the corrected entry in the reference list, not the joss branch used for this review.

[crvernon]

@editorialbot generate pdf

[crvernon]

@editorialbot set 10.5281/zenodo.13323298 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13323298

[editorialbot]

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

[crvernon]

@editorialbot set 0.8.1 as version

[editorialbot]

Done! version is now 0.8.1

[crvernon]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1017/CBO9780511720758 is OK
- 10.3726/978-3-653-01120-3 is OK
- 10.5089/9781484354841.069 is OK
- 10.5089/9781589063044.069 is OK
- 10.32614/RJ-2021-038 is OK
- 10.32614/CRAN.package.IndexNumR is OK
- 10.32614/CRAN.package.cansim is OK
- 10.32614/CRAN.package.micEconIndex is OK
- 10.32614/CRAN.package.hpiR is OK
- 10.32614/CRAN.package.PriceIndices is OK
- 10.5281/zenodo.10110159 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: cpi
- No DOI given, and none found for title: Technical Guide for the For-hire Motor Carrier Fre...
- No DOI given, and none found for title: Technical Guide for the Couriers and Messengers Se...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[crvernon]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.1017/CBO9780511720758 is OK
- 10.3726/978-3-653-01120-3 is OK
- 10.5089/9781484354841.069 is OK
- 10.5089/9781589063044.069 is OK
- 10.32614/RJ-2021-038 is OK
- 10.32614/CRAN.package.IndexNumR is OK
- 10.32614/CRAN.package.cansim is OK
- 10.32614/CRAN.package.micEconIndex is OK
- 10.32614/CRAN.package.hpiR is OK
- 10.32614/CRAN.package.PriceIndices is OK
- 10.5281/zenodo.10110159 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: cpi
- No DOI given, and none found for title: Technical Guide for the For-hire Motor Carrier Fre...
- No DOI given, and none found for title: Technical Guide for the Couriers and Messengers Se...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#5839, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

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: Martin
  given-names: Steve
  orcid: "https://orcid.org/0000-0003-2544-9480"
doi: 10.5281/zenodo.13323298
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Martin
    given-names: Steve
    orcid: "https://orcid.org/0000-0003-2544-9480"
  date-published: 2024-09-06
  doi: 10.21105/joss.06781
  issn: 2475-9066
  issue: 101
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6781
  title: "piar: Price Index Aggregation in R"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06781"
  volume: 9
title: "piar: Price Index Aggregation in R"

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]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06781 joss-papers#5858
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06781
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[crvernon]

🥳 Congratulations on your new publication @marberts! Many thanks to @schneiderpy and @realxinzhao 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]

🎉🎉🎉 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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reStructuredText:
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This is how it will look in your documentation:

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The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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[schneiderpy]

Also congratulations from my side

[marberts]

Thanks @crvernon for all your editorial work, and thanks @schneiderpy @realxinzhao for taking the time to review and give feedback. I really appreciate it!

[schneiderpy]

Thank you @crvernon, @marberts for letting me take part and for my first review and the new experiences I was able to gather

[schneiderpy]

@crvernon: one last question .. how can I add this review to my ORCID (since I am not allowed to add reviews manually)?