[REVIEW]: StormR: An R package to quantify and map the tropical storms and cyclones’ winds characteristics #5766

editorialbot · 2023-08-17T14:09:34Z

Submitting author: @thomasarsouze (Thomas Arsouze)
Repository: https://github.com/umr-amap/StormR
Branch with paper.md (empty if default branch):
Version: v0.1.2
Editor: @hugoledoux
Reviewers: @gsapijaszko, @highamm
Archive: 10.5281/zenodo.10417763

Status

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Markdown: [![status](https://joss.theoj.org/papers/774028082ef61ffc3474118bf96fef84/status.svg)](https://joss.theoj.org/papers/774028082ef61ffc3474118bf96fef84)

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Checklists

📝 Checklist for @highamm

📝 Checklist for @gsapijaszko

The text was updated successfully, but these errors were encountered:

editorialbot · 2023-08-17T14:09:36Z

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editorialbot · 2023-08-17T14:09:38Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (1204.2 files/s, 325159.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               18           1101           1990           4592
Markdown                         4            145              0            675
TeX                              1             26              0            351
YAML                             8             52             12            314
JSON                             1              0              0            117
Rmd                              6            170            642             74
-------------------------------------------------------------------------------
SUM:                            38           1494           2644           6123
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2023-08-17T14:09:40Z

Wordcount for paper.md is 1147

editorialbot · 2023-08-17T14:09:44Z

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

OK DOIs

- 10.1579/0044-7447(2008)37[241:TVOCWF]2.0.CO;2 is OK
- 10.1038/s41467-019-09319-2 is OK
- 10.1016/j.rsma.2022.102207 is OK
- 10.1038/s41467-021-21777-1 is OK
- 10.1017/9781009157896.002 is OK
- 10.1073/pnas.1922500117 is OK
- 10.1080/00431672.1974.9931702 is OK
- 10.25921/82ty-9e16 is OK
- 10.1175/2009BAMS2755.1 is OK
- 10.1175/MWR3106.1 is OK
- 10.1002/j.1477-8696.1999.tb06435.x is OK
- 10.1038/nature03906 is OK
- 10.1080/00431672.1974.9931702 is OK
- 10.1890/02-4057 is OK
- 10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2 is OK
- 10.1175/MWR2831.1 is OK
- 10.1175/1520-0493(1980)108<1212:AAMOTW>2.0.CO;2 is OK
- 10.1175/1520-0469(1995)052<4501:NMIOBV>2.0.CO;2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-08-17T14:11:18Z

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

highamm · 2023-08-18T16:09:58Z

Review checklist for @highamm

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/umr-amap/StormR?
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 (@thomasarsouze) 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?

highamm · 2023-08-21T14:08:12Z

Hi @thomasarsouze,

Would you be able to add the code generating the images in Figure 2 in https://github.com/umr-amap/StormR/tree/master/paper/images (or, if I've missed the code generating that Figure, could you point me in the right direction?)

Thanks!
Matt

highamm · 2023-08-21T14:09:20Z

Hi @thomasarsouze,

I've opened up an issue at umr-amap/StormR#68.

Thanks, and hope all is well!
Matt

thomasarsouze · 2023-08-31T10:54:11Z

Would you be able to add the code generating the images in Figure 2 in https://github.com/umr-amap/StormR/tree/master/paper/images (or, if I've missed the code generating that Figure, could you point me in the right direction?)

As stated in the caption of the figure, all plots were generated using plotStorms and plotBehaviour functions, and the code to produce them can be seen on this Spatial Behaviour article. However, they were gathered into one figure manualy.

highamm · 2023-08-31T11:26:54Z

Hey @thomasarsouze, thanks for the info! Would it be possible to add a link to the Spatial Behaviour article you reference in the Figure caption itself so that people reading the article know where to go to reproduce the sub-figures easily?

thomasarsouze · 2023-08-31T12:40:24Z

Hey @thomasarsouze, thanks for the info! Would it be possible to add a link to the Spatial Behaviour article you reference in the Figure caption itself so that people reading the article know where to go to reproduce the sub-figures easily?

Done in commit f25bf7b

highamm · 2023-09-01T17:29:32Z

Hello @thomasarsouze, can you add some community guidelines (clear guidelines for third parties wishing to 1. Contribute to the software, 2. Report issues or problems with the software, 3. Seek support) to the StormR repository README file?

Or, if these are given elsewhere, could you point me in the direction of where they are given? Thanks!

thomasarsouze · 2023-09-04T09:57:52Z

can you add some community guidelines (clear guidelines for third parties wishing to 1. Contribute to the software, 2. Report issues or problems with the software, 3. Seek support) to the StormR repository README file?

Indeed this is missing information.
Done in commit 38cb634

gsapijaszko · 2023-09-05T14:26:39Z

Review checklist for @gsapijaszko

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/umr-amap/StormR?
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 (@thomasarsouze) 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

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.)
Installation: Does installation proceed as outlined in the documentation?

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?

kthyng · 2023-10-25T17:40:32Z

Hi all! It looks like this review has grown stale. @gsapijaszko have you run across any issues in your review?

gsapijaszko · 2023-10-29T18:13:22Z

Hi,

I'm really sorry it took so long. Went through the review during the weekend, in my humble opinion, the paper is well written and can be published.

Regards,
Grzegorz

hugoledoux · 2023-11-07T13:31:39Z

Thanks @gsapijaszko for coming back to us.

You only mention the "paper", but JOSS is mostly about the code, the docs, and all the criteria as listed above. Can you let us know whether you installed the software and tested all the criteria? I am a bit confused by your wording here.

thomasarsouze · 2023-11-17T17:17:52Z

@hugoledoux & @kthyng : sorry to bother you, but is there anything we can do here to not let this review last too long ?

kthyng · 2023-11-20T18:21:41Z

@gsapijaszko Could you check in on this review please? See question above.

thomasarsouze · 2023-12-12T10:01:51Z

Hi.
It's been almost four months since submission, and I am not sure that the review process is still active.
Can you let us how to move on and finalize the review process ?
Sincerly

kthyng · 2023-12-13T22:18:40Z

@thomasarsouze I am sorry for the delay here. I have just emailed @gsapijaszko to see if we might hear back about their review to see about next steps. Thank you.

gsapijaszko · 2023-12-15T13:30:13Z

Yes, I have installed and tested the software. Otherwise I wouldn't mark check marks in review. Yes, I went through examples/help and played with the data. All criteria are met. I don't have anything to complain about, neither paper, neither software.

Regards,
Grzegorz

hugoledoux · 2023-12-22T14:57:40Z

@editorialbot set 10.5281/zenodo.10417763 as archive

editorialbot · 2023-12-22T14:57:42Z

Done! archive is now 10.5281/zenodo.10417763

hugoledoux · 2023-12-22T14:58:11Z

@editorialbot set v0.1.2 as version

hugoledoux · 2023-12-22T14:58:24Z

@editorialbot recommend-accept

editorialbot · 2023-12-22T14:58:26Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-12-22T14:59:01Z

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

OK DOIs

- 10.1579/0044-7447(2008)37[241:TVOCWF]2.0.CO;2 is OK
- 10.1038/s41467-019-09319-2 is OK
- 10.1016/j.rsma.2022.102207 is OK
- 10.1038/s41467-021-21777-1 is OK
- 10.1017/9781009157896.002 is OK
- 10.1073/pnas.1922500117 is OK
- 10.1080/00431672.1974.9931702 is OK
- 10.25921/82ty-9e16 is OK
- 10.1175/2009BAMS2755.1 is OK
- 10.1175/MWR3106.1 is OK
- 10.1002/j.1477-8696.1999.tb06435.x is OK
- 10.1038/nature03906 is OK
- 10.1080/00431672.1974.9931702 is OK
- 10.1890/02-4057 is OK
- 10.1890/0012-9615(2001)071[0027:LARIOH]2.0.CO;2 is OK
- 10.1175/MWR2831.1 is OK
- 10.1175/1520-0493(1980)108<1212:AAMOTW>2.0.CO;2 is OK
- 10.1175/1520-0469(1995)052<4501:NMIOBV>2.0.CO;2 is OK

MISSING DOIs

- None

INVALID DOIs

- None

hugoledoux · 2023-12-22T14:59:59Z

@thomasarsouze it took longer than what we wanted, but in the end it's accepted just in time for the winter holidays 🎄☃️

thanks to @gsapijaszko and @highamm !

editorialbot · 2023-12-22T15:00:12Z

👋 @openjournals/ese-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#4863, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

kthyng · 2024-01-02T17:29:00Z

My steps:

Check that version was updated
Check that software archive exists, has been input to JOSS, and title and author list look good
Check paper

kthyng · 2024-01-02T17:32:00Z

@editorialbot set v0.1.2 as version

editorialbot · 2024-01-02T17:32:02Z

Done! version is now v0.1.2

kthyng · 2024-01-02T17:35:44Z

Not sure why that didn't stick before...

kthyng · 2024-01-02T17:39:54Z

@thomasarsouze A JOSS review is usually a good time to bump to a nice round version number like v1.0.0 — but up to you.

kthyng · 2024-01-02T17:48:29Z

Paper edits: umr-amap/StormR#79

thomasarsouze · 2024-01-09T14:29:55Z

@kthyng thanks for your inputs, they have been merged.

A JOSS review is usually a good time to bump to a nice round version number like v1.0.0 — but up to you.

I prefer to stick to the current version, we have long-term developments that will later justify such a bump.

kthyng · 2024-01-11T14:52:11Z

@editorialbot generate pdf

editorialbot · 2024-01-11T14:53:22Z

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

kthyng · 2024-01-11T14:57:07Z

Ok looks ready to go!

kthyng · 2024-01-11T14:57:11Z

@editorialbot accept

editorialbot · 2024-01-11T14:57:13Z

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

editorialbot · 2024-01-11T15:04:29Z

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: Delaporte
  given-names: Baptiste
- family-names: Arsouze
  given-names: Thomas
  orcid: "https://orcid.org/0000-0002-8871-6120"
- family-names: Keppel
  given-names: Gunnar
  orcid: "https://orcid.org/0000-0001-7092-6149"
- family-names: Jullien
  given-names: Swen
  orcid: "https://orcid.org/0000-0002-5389-0532"
- family-names: Menkes
  given-names: Christophe
  orcid: "https://orcid.org/0000-0002-1457-9696"
- family-names: Ibanez
  given-names: Thomas
  orcid: "https://orcid.org/0000-0002-3192-1721"
contact:
- family-names: Arsouze
  given-names: Thomas
  orcid: "https://orcid.org/0000-0002-8871-6120"
doi: 10.5281/zenodo.10417763
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Delaporte
    given-names: Baptiste
  - family-names: Arsouze
    given-names: Thomas
    orcid: "https://orcid.org/0000-0002-8871-6120"
  - family-names: Keppel
    given-names: Gunnar
    orcid: "https://orcid.org/0000-0001-7092-6149"
  - family-names: Jullien
    given-names: Swen
    orcid: "https://orcid.org/0000-0002-5389-0532"
  - family-names: Menkes
    given-names: Christophe
    orcid: "https://orcid.org/0000-0002-1457-9696"
  - family-names: Ibanez
    given-names: Thomas
    orcid: "https://orcid.org/0000-0002-3192-1721"
  date-published: 2024-01-11
  doi: 10.21105/joss.05766
  issn: 2475-9066
  issue: 93
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 5766
  title: "StormR: An R package to quantify and map the tropical storms
    and cyclones' winds characteristics"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.05766"
  volume: 9
title: "StormR: An R package to quantify and map the tropical storms and
  cyclones' winds characteristics"

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 · 2024-01-11T15:04:33Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2024-01-11T15:04:34Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.05766 joss-papers#4896
Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.05766
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng · 2024-01-11T15:09:12Z

Congrats on your new publication @thomasarsouze! Many thanks to editor @hugoledoux and reviewers @gsapijaszko and @highamm for your time, hard work, and expertise!!

editorialbot · 2024-01-11T15:09:14Z

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

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HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.05766/status.svg" alt="DOI badge" >
</a>

reStructuredText:
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   :target: https://doi.org/10.21105/joss.05766

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editorialbot added R review TeX Track: 6 (ESE) Earth Sciences and Ecology waitlisted Submissions in the JOSS backlog due to reduced service mode. labels Aug 17, 2023

editorialbot assigned hugoledoux Aug 17, 2023

editorialbot mentioned this issue Aug 17, 2023

[PRE REVIEW]: StormR: An R package to quantify and map the tropical storms and cyclones’ winds characteristics #5725

Closed

kthyng removed the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Oct 25, 2023

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Dec 22, 2023

kthyng mentioned this issue Jan 2, 2024

Paper edits umr-amap/StormR#79

Merged

editorialbot added accepted published Papers published in JOSS labels Jan 11, 2024

kthyng closed this as completed Jan 11, 2024

[REVIEW]: StormR: An R package to quantify and map the tropical storms and cyclones’ winds characteristics #5766

[REVIEW]: StormR: An R package to quantify and map the tropical storms and cyclones’ winds characteristics #5766

Comments

editorialbot commented Aug 17, 2023 • edited

Status

Reviewer instructions & questions

Checklists

editorialbot commented Aug 17, 2023

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highamm commented Aug 18, 2023 • edited

Review checklist for @highamm

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

highamm commented Aug 21, 2023

highamm commented Aug 21, 2023

thomasarsouze commented Aug 31, 2023

highamm commented Aug 31, 2023

thomasarsouze commented Aug 31, 2023

highamm commented Sep 1, 2023

thomasarsouze commented Sep 4, 2023

gsapijaszko commented Sep 5, 2023 • edited

Review checklist for @gsapijaszko

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

kthyng commented Oct 25, 2023

gsapijaszko commented Oct 29, 2023

hugoledoux commented Nov 7, 2023

thomasarsouze commented Nov 17, 2023

kthyng commented Nov 20, 2023

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kthyng commented Dec 13, 2023

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editorialbot commented Aug 17, 2023 •

edited

highamm commented Aug 18, 2023 •

edited

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edited

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edited

kthyng commented Jan 2, 2024 •

edited