[REVIEW]: RMAVIS v1.0: a R Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities

[editorialbot]

Submitting author: @ZekeMarshall (Zeke Marshall)
Repository: https://github.com/ZekeMarshall/RMAVIS/
Branch with paper.md (empty if default branch): main
Version: v1.0
Editor: @mikemahoney218
Reviewers: @adithirgis, @rasanderson
Archive: Pending

Status

Status badge code:

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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

@adithirgis & @rasanderson, 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 @rasanderson

[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:

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.06 s (1118.4 files/s, 323283.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               51           3011           1140           8277
HTML                             2            548             12           3069
TeX                              4            131              0           1333
Markdown                         4            154              0            649
Rmd                              4            489            895            496
CSS                              1             39             23            114
YAML                             3             14              6             68
Dockerfile                       1              6              7             23
JSON                             1              0              0             19
-------------------------------------------------------------------------------
SUM:                            71           4392           2083          14048
-------------------------------------------------------------------------------

Commit count by author:

   184	ZekeMarshall
     1	Zeke Marshall

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1179

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🔴 License found: Creative Commons Attribution 4.0 International (Not OSI approved)

[editorialbot]

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

OK DOIs

- 10.1111/rec.13035 is OK
- 10.1007/BF00031691 is OK
- 10.1111/ecog.06547 is OK
- 10.1111/avsc.12516 is OK
- 10.33928/bib.2023.05.001 is OK
- 10.1046/j.1365-2664.2002.00718.x is OK
- 10.1007/s11258-020-01016-1 is OK
- 10.1017/9780521235587 is OK
- 10.1017/9780521391658 is OK
- 10.1017/9780521391665 is OK
- 10.1017/9781107340817 is OK
- 10.1017/CBO9780511541834 is OK
- 10.1023/a:1008948602316 is OK
- 10.5285/42C203C8-44DE-40E2-A694-B1E8CBD4C8E1 is OK
- 10.1002/ecs2.4726 is OK
- 10.5194/essd-7-203-2015 is OK

MISSING DOIs

- No DOI given, and none found for title: Ellenberg indicator F (moisture)
- No DOI given, and none found for title: Ellenberg indicator L (light)
- No DOI given, and none found for title: Ellenberg indicator N (nitrogen)
- No DOI given, and none found for title: Ellenberg indicator R (reaction)
- No DOI given, and none found for title: Ellenberg indicator S (salt tolerance)
- No DOI given, and none found for title: Taxon lists Botanical Society of Britain & Ireland
- No DOI given, and none found for title: Vegetation of the British Countryside - the Countr...
- No DOI given, and none found for title: UK Habitats Classification User Manual Version 1.1
- No DOI given, and none found for title: shiny: Web Application Framework for R
- No DOI given, and none found for title: Guidelines For Ecological Impact Assessment In The...
- No DOI given, and none found for title: BRYOATT - Attributes of British and Irish Mosses, ...
- No DOI given, and none found for title: Spreadsheet of Habitat Correspondences
- No DOI given, and none found for title: MATCH version 2
- No DOI given, and none found for title: TABLEFIT v. 3.0 & v.4, Programs for the Identifica...
- No DOI given, and none found for title: The Irish Vegetation Classification - an Overview ...
- No DOI given, and none found for title: ERICA - Engine for Relevés to Irish Communities As...
- No DOI given, and none found for title: S1 File
- No DOI given, and none found for title: National vegetation classification: Users’ handboo...
- No DOI given, and none found for title: MAVIS (Ver 1.03) User Manual
- No DOI given, and none found for title: A review of the National Vegetation Classification...
- No DOI given, and none found for title: Monitoring of forest removal and groundworks to re...
- No DOI given, and none found for title: An Exploration of Oceanic Wet Grasslands in the Sc...

INVALID DOIs

- None

[editorialbot]

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

[mikemahoney218]

👋🏼 @ZekeMarshall, @adithirgis, @rasanderson this is the review thread for the paper. 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.

These checklists contain the JOSS 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#6615 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 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.

[rasanderson]

Review checklist for @rasanderson

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/ZekeMarshall/RMAVIS/?
• 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 (@ZekeMarshall) 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]

@ZekeMarshall , I just noticed that you changed the license of the project a few days ago to a non open-source license. JOSS only reviews projects that are open source using an OSI-approved license (as mentioned on the first bullet point on the 'Submission requirements' checklist), which none of the creative commons licenses are (and CC recommends against using their licenses for software). Is there a reason you changed away from the MIT license? We will not be able to accept the project using the current (CC-BY) license.

[ZekeMarshall]

Hi @mikemahoney218 , apologies for this! I neglected to check that CCBY4.0 wasn't OSI-approved. I'll change this again in the morning when i'm in the office, likely to AAL, we just wanted to ensure attribution. PS thank you @adithirgis and @rasanderson for agreeing to review!

[ZekeMarshall]

Hi @mikemahoney218 , I've now changed the licence to the OSI-approved LGPL 3.0 and made a new release. Could you set the version to v0.9995? Thanks!

[mikemahoney218]

Thanks @ZekeMarshall ! I believe we don't need to update the version until we accept the package -- feel free to bump it and release new ones whenever is convenient for you.

[ZekeMarshall]

@editorialbot generate pdf

[editorialbot]

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

[ZekeMarshall]

Hi @rasanderson & @adithirgis, I've bumped the version to v0.9996. This version includes a few minor changes and one more substantial change, namely using the NBN to form the taxonomic backbone for vascular plants as well as bryophytes, so now there is only one source for the taxonomic backbone.

[ZekeMarshall]

Hi @rasanderson & @adithirgis, I've bumped the version to v0.9997. This version sets R 4.4 as the minimum version in response to the reported 'non-vulnerability' in R wherein arbitrary code can be executed when de-serialising R data objects, see here, which is not in fact fixed by R 4.4.0.

[mikemahoney218]

Just as a quick note: I'm going to be traveling and generally less available until May 20th. I'll still be checking GitHub and email intermittently (so feel free to reach out with any questions or concerns), but apologies if it takes me a bit longer to respond than usual!

[ZekeMarshall]

Just as a quick note: I'm going to be traveling and generally less available until May 20th. I'll still be checking GitHub and email intermittently (so feel free to reach out with any questions or concerns), but apologies if it takes me a bit longer to respond than usual!

Thanks for letting us know and no worries at all. Have a good break!

[rasanderson]

Thanks for letting us know. I hope to have some first comments back fairly soon, so apologies for slight delay.

[ZekeMarshall]

@editorialbot set https://github.com/NERC-CEH/RMAVIS as repository

[editorialbot]

I'm sorry @ZekeMarshall, I'm afraid I can't do that. That's something only editors are allowed to do.

[ZekeMarshall]

Hi @mikemahoney218 , I've transferred the RMAVIS repository to our organisations Github (https://github.com/NERC-CEH/RMAVIS), would you be able to set this as the repository?