[REVIEW]: aion: An R Package to Represent Archaeological Time Series

[editorialbot]

Submitting author: @nfrerebeau (Nicolas Frerebeau)
Repository: https://github.com/tesselle/aion
Branch with paper.md (empty if default branch):
Version: v1.0.3
Editor: @martinfleis
Reviewers: @sebastien-plutniak, @steko
Archive: 10.5281/zenodo.10926190

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/5a1891dd6acef84a706cb1cb250858fd/status.svg)](https://joss.theoj.org/papers/5a1891dd6acef84a706cb1cb250858fd)

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

@sebastien-plutniak & @steko, 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 @martinfleis 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 @steko

📝 Checklist for @sebastien-plutniak

[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:

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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 1.88  T=0.06 s (1400.0 files/s, 108375.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                              9              0              0           1388
R                               44            297           1209           1353
Markdown                        14            245              0            829
JSON                             1              0              0            199
Rmd                              4            102            207            132
TeX                              2              0              0            116
YAML                             6             12              7             97
-------------------------------------------------------------------------------
SUM:                            80            656           1423           4114
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 632

[editorialbot]

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

OK DOIs

- 10.18637/jss.v093.c01 is OK
- 10.1111/j.1467-9876.2008.00623.x is OK
- 10.5281/zenodo.5653896 is OK
- 10.1017/RDC.2020.95 is OK
- 10.21105/joss.05337 is OK
- 10.18637/jss.v014.i06 is OK
- 10.1017/9781107415058 is OK
- 10.5334/jcaa.29 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[martinfleis]

👋🏼 @nfrerebeau, @sebastien-plutniak, @steko this is the review thread for the paper. All of our communications will happen here from now on.

All reviewers should create checklists with the JOSS requirements using the command @editorialbot generate my checklist. 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 small pull requests if needed) on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6210 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, feel free to start whenever it works for you. Please let me know if any of you require significantly more time at any point. We can also use editorialbot to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@martinfleis) if you have any questions/concerns.

Thanks!

[steko]

Review checklist for @steko

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/tesselle/aion?
• 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 (@nfrerebeau) 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?

[martinfleis]

Hi @sebastien-plutniak, @steko, could you provide a short update on the progress of the review? Thanks!

[steko]

@editorialbot generate pdf

[editorialbot]

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

[martinfleis]

@editorialbot remind @sebastien-plutniak in one week

[editorialbot]

Reminder set for @sebastien-plutniak in one week

[martinfleis]

@editorialbot remind @steko in one week

[editorialbot]

Reminder set for @steko in one week

[sebastien-plutniak]

Review checklist for @sebastien-plutniak

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/tesselle/aion?
• 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 (@nfrerebeau) 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?

[sebastien-plutniak]

Disclaimer: although the author and I do not directly collaborate on scientific products (leading projects, co-authoring papers, etc.) we both are part of the small community of archeologists interested in computer applications in France and have contact in this context. This fact does not seem to conflict with JOSS COI policy.

After reviewing it, this submission seems almost ready for publication in JOSS. The paper and the package documentation are clear, well structured, and including a sufficient number of examples. Small improvements might be suggested, including:

• adding automated tests
• adding community guidelines (note that a code of conduct is already present)
  Regarding the quality of writing, it looks correct to me, but English is not my primary language so I cannot judge it.

Additional suggestion: it might be interesting to add examples (with code) of how aion can make interoperable formats used by other packages.

[editorialbot]

👋 @sebastien-plutniak, please update us on how your review is going (this is an automated reminder).

[editorialbot]

👋 @steko, please update us on how your review is going (this is an automated reminder).

[nfrerebeau]

* adding automated tests

There are automated tests, but aion uses tinytest instead of testthat. Tests can be run with tinytest::run_test_dir() or devtools::check() (devtools::test() won't work, as it relies on testthat).

* adding community guidelines (note that a code of conduct is already present)

Community guidelines are available on the project website (https://www.tesselle.org/contributing.html) and in the repository (https://github.com/tesselle/aion/blob/main/.github/CONTRIBUTING.md).

Additional suggestion: it might be interesting to add examples (with code) of how aion can make interoperable formats used by other packages.

That's a good point. However, it's going to take me some time to find a real use case. I've just opened an issue to track progress on that (tesselle/aion#4).

[martinfleis]

@nfrerebeau is it a correct understanding that we are currently waiting for tesselle/aion#4 before @sebastien-plutniak can close their review?

[martinfleis]

@steko could you let me know the status of your review? I see the checklist is partially filled but am not sure about the status of the missing points. Thanks!

[martinfleis]

@editorialbot set 10.5281/zenodo.10926190 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10926190

[editorialbot]

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

[martinfleis]

@editorialbot set v1.0.3 as version

[editorialbot]

Done! version is now v1.0.3

[martinfleis]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[martinfleis]

Thank you @nfrerebeau! The final steps are on the editor-in-chief who'll be notified.

[editorialbot]

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

OK DOIs

- 10.18637/jss.v093.c01 is OK
- 10.1111/j.1467-9876.2008.00623.x is OK
- 10.5281/zenodo.5653896 is OK
- 10.1017/RDC.2020.95 is OK
- 10.21105/joss.05337 is OK
- 10.18637/jss.v014.i06 is OK
- 10.1017/9781107415058 is OK
- 10.5334/jcaa.29 is OK

MISSING DOIs

- No DOI given, and none found for title: era: Year-Based Time Scales
- No DOI given, and none found for title: Introducing an R package for luminescence dating a...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...

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#5209, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[oliviaguest]

@nfrerebeau can you amend the double parentheses please? So things like (e.g., Bchron by Haslett & Parnell (2008) or rcarbon by Crema & Bevan (2021)) become something like (e.g., Bchron by Haslett & Parnell, 2008; or rcarbon by Crema & Bevan, 2021). If you don't know how to do it: remove the square brackets. ☺️

[nfrerebeau]

@oliviaguest Done! (tesselle/aion@ca67754)

[oliviaguest]

@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

- 10.18637/jss.v093.c01 is OK
- 10.1111/j.1467-9876.2008.00623.x is OK
- 10.5281/zenodo.5653896 is OK
- 10.1017/RDC.2020.95 is OK
- 10.21105/joss.05337 is OK
- 10.18637/jss.v014.i06 is OK
- 10.1017/9781107415058 is OK
- 10.5334/jcaa.29 is OK

MISSING DOIs

- No DOI given, and none found for title: era: Year-Based Time Scales
- No DOI given, and none found for title: Introducing an R package for luminescence dating a...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...

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#5235, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[steko]

Would it be possible to have my name as reviewer link to ORCID and not GitHub? Thanks!

[oliviaguest]

@steko I do not think so, sorry. I will ask @arfon, but I suspect there is a good reason for this. You may link your GitHub account to your ORCID to help people find you (which I see you do already do), but I am not sure what else can be done.

[arfon]

Yeah, I'm afraid this (linking to ORCIDs for reviewers) isn't currently supported sorry.

[oliviaguest]

@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: Frerebeau
  given-names: Nicolas
  orcid: "https://orcid.org/0000-0001-5759-4944"
doi: 10.5281/zenodo.10926190
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Frerebeau
    given-names: Nicolas
    orcid: "https://orcid.org/0000-0001-5759-4944"
  date-published: 2024-04-11
  doi: 10.21105/joss.06210
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6210
  title: "aion: An R Package to Represent Archaeological Time Series"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06210"
  volume: 9
title: "aion: An R Package to Represent Archaeological Time Series"

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.06210 joss-papers#5238
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06210
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...

[oliviaguest]

Huge thanks to the reviewers @sebastien-plutniak, @steko, and editor, @martinfleis! ✨ JOSS appreciates your work and effort. ✨ Also, big congratulations to the authors @nfrerebeau! 🥳 🍾

[editorialbot]

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

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