[REVIEW]: growR: R Implementation of the Vegetation Model ModVege

[editorialbot]

Submitting author: @kuadrat (Kevin Kramer)
Repository: https://github.com/kuadrat/growR
Branch with paper.md (empty if default branch): joss
Version: growR-1.2.0-JOSS
Editor: @mikemahoney218
Reviewers: @shubhamjain15, @RobLBaker
Archive: 10.5281/zenodo.10658193

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/bd4b3a207a8d4de1dc784dba702e38fc"><img src="https://joss.theoj.org/papers/bd4b3a207a8d4de1dc784dba702e38fc/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/bd4b3a207a8d4de1dc784dba702e38fc/status.svg)](https://joss.theoj.org/papers/bd4b3a207a8d4de1dc784dba702e38fc)

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

@shubhamjain15 & @RobLBaker, 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 @mikemahoney218 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 @shubhamjain15

📝 Checklist for @RobLBaker

[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:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (928.4 files/s, 137092.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               31            326           2459           2521
TeX                              2             36              0            488
SVG                              2              2              2            433
Markdown                         4            103              0            361
YAML                             5             21              8            204
Rmd                              8            151            497             67
-------------------------------------------------------------------------------
SUM:                            52            639           2966           4074
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 898

[editorialbot]

Failed to discover a Statement of need section in paper

[editorialbot]

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

OK DOIs

- 10.1007/s10980-020-00980-3 is OK
- 10.1073/pnas.1308149110 is OK
- 10.1007/s10980-020-00980-3 is OK
- 10.1006/anbo.1997.0430 is OK
- 10.1017/S0021859600067290 is OK
- 10.1111/j.1365-2494.2006.00515.x is OK
- 10.1016/j.eja.2018.06.010 is OK
- 10.1016/j.jafr.2023.100875 is OK
- 10.1016/j.fcr.2015.12.008 is OK
- 10.1016/j.eja.2021.126306 is OK
- 10.1016/j.agrformet.2017.05.017 is OK
- 10.1016/j.jhydrol.2007.10.052 is OK
- 10.1111/j.1752-1688.1995.tb03392.x is OK
- 10.1016/j.ecolmodel.2019.108925 is OK
- 10.5281/zenodo.27867 is OK
- 10.1016/S0308-521X(97)00023-1 is OK
- 10.1016/j.ecolmodel.2008.11.023 is OK
- 10.1016/j.agee.2011.07.001 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1017/9781009325844.007.714 is INVALID

[editorialbot]

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

[mikemahoney218]

👋🏼 @kuadrat , @shubhamjain15 , @RobLBaker , this is the review thread for {growR}. Just about all of our communications will happen here from now on 😄 .

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread. For best results, don't include anything else in the comment!

This will create a checklist that walks through the JOSS submission requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains 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 openjournals/joss-reviews#6260 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. Please let me know if you require some more time.

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns.

Thank you so much for agreeing to review this submission!

[mikemahoney218]

@editorialbot remind @mikemahoney218 in 2 weeks

(Setting up an automated reminder for myself to make sure this doesn't fall through the cracks 😄 )

[editorialbot]

Reminder set for @mikemahoney218 in 2 weeks

[shubhamjain15]

Review checklist for @shubhamjain15

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/kuadrat/growR?
• 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 (@kuadrat) 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?

[mikemahoney218]

👋 @kuadrat , @shubhamjain15 , and @RobLBaker , just wanted to share that I'm going to be OOO from February 2nd through the 9th (so, Friday through the end of next week). I'll be around somewhat but will be much more delayed in responding on this issue; apologies in advance!

And as always, feel free to reach out if you have any questions or concerns 😄

[editorialbot]

👋 @mikemahoney218, please take a look at the state of the submission (this is an automated reminder).

[kuadrat]

Regarding license (as I can see this is an unchecked box in the review checklist of @shubhamjain15 ), please have a look at the discussion that has already occurred during pre-review and links therein:

#6176 (comment)

In short: At the moment it does not seem to be possible to simultaneously satisfy CRAN's and github's conventions regarding naming and structure of license files. Since the main avenue of distribution is via CRAN, the choice has been made to follow their conventions. The conclusion in JOSS reviews for other R packages has been that this complies with JOSS (see linked comment).

[RobLBaker]

Review checklist for @RobLBaker

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/kuadrat/growR?
• 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 (@kuadrat) 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 📄 👈

[RobLBaker]

Really cool work!

I missed the statement of need in the Documentation. I am assuming this is separate from the statement of need in the Software paper. Perhaps I'm overlooking it somewhere - if you could please point me in the right direction or confirm that these two statements of need are one and the same, I'd be happy to check that last box.

[mikemahoney218]

@shubhamjain15 , I see that your checklist is all filled in -- are you finished reviewing the package?

[mikemahoney218]

(and @kuadrat , if I'm not mistaken, I think ☝️ from Rob is the last outstanding issue on this review!)

[shubhamjain15]

@mikemahoney218 Hello Mike! I completed my review yesterday, and in my assessment, this submission meets all the points on the check list. :)

[mikemahoney218]

Thank you so much @shubhamjain15 !

[kuadrat]

Dear @shubhamjain15 , @RobLBaker ,

thank you very much for your review efforts! I'm very glad to hear that the package is received mostly positively.

@RobLBaker I have extended the README with a What is this for? section on the joss branch. Once I merge this into master, the docs will be updated accordingly. It is essentially a slightly less formal rewording of relevant paragraphs in the paper. Please let me know what you think.

[RobLBaker]

Works for me - I checked that last box. Please let me know if there's anything else needed from me & happy to review more submissions, especially if they're of this quality.

[editorialbot]

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

OK DOIs

- 10.1007/s10980-020-00980-3 is OK
- 10.1073/pnas.1308149110 is OK
- 10.1007/s10980-020-00980-3 is OK
- 10.1017/9781009325844.007 is OK
- 10.1006/anbo.1997.0430 is OK
- 10.1017/S0021859600067290 is OK
- 10.1111/j.1365-2494.2006.00515.x is OK
- 10.1016/j.eja.2018.06.010 is OK
- 10.1016/j.jafr.2023.100875 is OK
- 10.1016/j.fcr.2015.12.008 is OK
- 10.1016/j.eja.2021.126306 is OK
- 10.1016/j.agrformet.2017.05.017 is OK
- 10.1016/j.jhydrol.2007.10.052 is OK
- 10.1111/j.1752-1688.1995.tb03392.x is OK
- 10.1016/j.ecolmodel.2019.108925 is OK
- 10.5281/zenodo.27867 is OK
- 10.1016/S0308-521X(97)00023-1 is OK
- 10.1016/j.ecolmodel.2008.11.023 is OK
- 10.1016/j.agee.2011.07.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-zhao2020GrasslandEcosystemServices already defined

[mikemahoney218]

@kuadrat Looks like you've got a duplicate entry for zhao2020GrasslandEcosystemServices in your bibtex (first and third entries) -- at a glance, they appear to be identical. Can you remove one of those?

[kuadrat]

I removed the duplicate and checked all other entries for uniqueness.
Fingers crossed.

[mikemahoney218]

@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

- 10.1073/pnas.1308149110 is OK
- 10.1007/s10980-020-00980-3 is OK
- 10.1017/9781009325844.007 is OK
- 10.1006/anbo.1997.0430 is OK
- 10.1017/S0021859600067290 is OK
- 10.1111/j.1365-2494.2006.00515.x is OK
- 10.1016/j.eja.2018.06.010 is OK
- 10.1016/j.jafr.2023.100875 is OK
- 10.1016/j.fcr.2015.12.008 is OK
- 10.1016/j.eja.2021.126306 is OK
- 10.1016/j.agrformet.2017.05.017 is OK
- 10.1016/j.jhydrol.2007.10.052 is OK
- 10.1111/j.1752-1688.1995.tb03392.x is OK
- 10.1016/j.ecolmodel.2019.108925 is OK
- 10.5281/zenodo.27867 is OK
- 10.1016/S0308-521X(97)00023-1 is OK
- 10.1016/j.ecolmodel.2008.11.023 is OK
- 10.1016/j.agee.2011.07.001 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @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#5015, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[mikemahoney218]

🎉 looks like it went through that time, which means it's time for me to hand this back to the EiC for last steps. Thanks @kuadrat for the submission, and thank you so much to @shubhamjain15 and @RobLBaker for reviewing!

[kuadrat]

Many thanks from my side to @shubhamjain15, @RobLBaker and @mikemahoney218 for putting in the time and work into this review process!

[kthyng]

Hi all! My job is to help wrap up this submission and do some final checks.

First, one question for @shubhamjain15 and @RobLBaker: can you verify that you installed the software and got it to run, etc? I ask because it's a bit unusual to have reviews go this quickly and not require any issues being opened on the software repo. It happens occasionally, but just want to check in to make sure the process was clear to everyone given the circumstances. Thank you!

[RobLBaker]

Yes, I was able to download and install the package. It appears to function as claimed: I was able to recreate all of the analyses and results from the Tutorial and Calibration vignettes using the example data.

[kthyng]

@RobLBaker Thank you for your response to my unusual request!

@shubhamjain15 Could you confirm the same?

[shubhamjain15]

Hi Kristen! Yes I was able to install the R package and use the examples in the reference manual and tutorial to test the functionality successfully.

[kthyng]

Ok great! This being an easy submission to review really says a lot for @kuadrat's effort on the package.

[kthyng]

Here is my to do list:

• 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]

Everything is ready to go.

[kthyng]

@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: Kramer
  given-names: Kevin P.
  orcid: "https://orcid.org/0000-0001-5523-6924"
- family-names: Calanca
  given-names: Pierluigi
  orcid: "https://orcid.org/0000-0003-3113-2885"
contact:
- family-names: Kramer
  given-names: Kevin P.
  orcid: "https://orcid.org/0000-0001-5523-6924"
doi: 10.5281/zenodo.10658193
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Kramer
    given-names: Kevin P.
    orcid: "https://orcid.org/0000-0001-5523-6924"
  - family-names: Calanca
    given-names: Pierluigi
    orcid: "https://orcid.org/0000-0003-3113-2885"
  date-published: 2024-02-15
  doi: 10.21105/joss.06260
  issn: 2475-9066
  issue: 94
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6260
  title: "growR: R Implementation of the Vegetation Model ModVege"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06260"
  volume: 9
title: "growR: R Implementation of the Vegetation Model ModVege"

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.06260 joss-papers#5017
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06260
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...

[kthyng]

Congrats on your new publication @kuadrat! Many thanks to editor @mikemahoney218 and reviewers @shubhamjain15 and @RobLBaker for your time, hard work, and expertise!!

[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:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06260/status.svg)](https://doi.org/10.21105/joss.06260)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06260">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06260/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06260/status.svg
   :target: https://doi.org/10.21105/joss.06260

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:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
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[kuadrat]

Congrats on your new publication @kuadrat! Many thanks to editor @mikemahoney218 and reviewers @shubhamjain15 and @RobLBaker for your time, hard work, and expertise!!

Many thanks also to all of you for your voluntary work!

I'm happy this went so smoothly. Maybe a remark on that note: Part of what likely helped making this submission go through without many issues is the fact that the package has been published on CRAN. This means that it has already undergone a number of automated and human-overseen quality checks before being submitted to JOSS.

[kthyng]

@kuadrat Thanks for that comment and that makes sense. I'll keep my eye out for that being a mitigating (and helpful!) factor on future reviews.

Also if you're interested in getting involved in JOSS, please consider signing up as a reviewer! https://reviewers.joss.theoj.org/