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

[editorialbot]

Submitting author: !--author-handle-->@ZekeMarshall<!--end-author-handle-- (Zeke Marshall) Repository: https://github.com/ZekeMarshall/RMAVIS/ Branch with paper.md (empty if default branch): main Version: v0.9992 Editor: !--editor-->@mikemahoney218<!--end-editor-- Reviewers: @adithirgis, @rasanderson Managing EiC: Kristen Thyng

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Thanks for submitting your paper to JOSS @ZekeMarshall. Currently, there isn't a JOSS editor assigned to your paper.

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[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1046/j.1365-2664.2002.00718.x is OK
- 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
- 10.1007/s11258-020-01016-1 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: Spreadsheet of Habitat Correspondences
- 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: 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: S1 File
- No DOI given, and none found for title: British Plant Communities Set of Volumes 1 to 5
- 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: BRYOATT - Attributes of British and Irish Mosses, ...

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.07 s (1035.1 files/s, 290868.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               51           3011           1139           8276
HTML                             2            548             12           3022
TeX                              4            127              0           1243
Rmd                              4            486            885            496
Markdown                         4             64              0            323
CSS                              1             39             23            114
YAML                             3             14              6             68
Dockerfile                       1              6              7             23
JSON                             1              0              0             19
-------------------------------------------------------------------------------
SUM:                            71           4295           2072          13584
-------------------------------------------------------------------------------

Commit count by author:

   174  ZekeMarshall
     1  Zeke Marshall

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1148

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[kthyng]

Hi @ZekeMarshall and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• [ ] Substantial scholarly effort
• [x] Documentation
• [x] Tests of some sort
• [ ] Installation instructions
• [ ] Clear research application
• [x] Check paper
• [x] License

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[kthyng]

Hi @ZekeMarshall you have two license files — the MIT one is what we'd normally expect but is there a reason you need both files?

[ZekeMarshall]

Hi @kthyng , thanks for taking a look at this so quickly!

Thanks for pointing out the surplus licence file, I've now removed this.

Just to check, is it ok to review from the v1 branch?

Here is my list of suggested reviewers:

• TahiriNadia
• ahasverus
• luciorq
• adithirgis
• kdm9

Thanks again!

[ZekeMarshall]

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

OK DOIs

- 10.1046/j.1365-2664.2002.00718.x is OK
- 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
- 10.1007/s11258-020-01016-1 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: Spreadsheet of Habitat Correspondences
- 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: 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: S1 File
- No DOI given, and none found for title: British Plant Communities Set of Volumes 1 to 5
- 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: BRYOATT - Attributes of British and Irish Mosses, ...

INVALID DOIs

- None

I've double-checked my list of references and only managed to replace one reference without a DOI, there are no DOI's for the others unfortunately!

[ZekeMarshall]

@editorialbot check references

[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...

INVALID DOIs

- None

[ZekeMarshall]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[ZekeMarshall]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[kthyng]

Just to check, is it ok to review from the v1 branch?

Yes that's fine, though I see it is out of date compared to the main branch now. Is there a reason for that? If you are actively developing it might be best to keep the branch up to date until the review starts, unless there is reason to keep the branch where it is for the review.

[kthyng]

@ZekeMarshall I am going to ping the editorial board to take a make sure this submission is in scope as a web application. This process will take 1-2 weeks. Thank you for your patience!

[kthyng]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[ZekeMarshall]

@ZekeMarshall I am going to ping the editorial board to take a make sure this submission is in scope as a web application. This process will take 1-2 weeks. Thank you for your patience!

Hi @kthyng , thanks, I hope it is within scope! Thanks again, Zeke

[ZekeMarshall]

Just to check, is it ok to review from the v1 branch?

Yes that's fine, though I see it is out of date compared to the main branch now. Is there a reason for that? If you are actively developing it might be best to keep the branch up to date until the review starts, unless there is reason to keep the branch where it is for the review.

Hi @kthyng , no problem! What i'll do is make a v0.999 release on the main branch to clean things up, then just use the main branch for the review. Thanks again, Zeke

[ZekeMarshall]

@editorialbot set main as branch

[editorialbot]

Done! branch is now main

[ZekeMarshall]

@editorialbot set v0.999 as version

[editorialbot]

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

[ZekeMarshall]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[ZekeMarshall]

Final set of updates pre-review!

@editorialbot generate pdf

[ZekeMarshall]

@editorialbot generate pdf

[editorialbot]

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

[kthyng]

@editorialbot set v0.999 as version

[editorialbot]

Done! version is now v0.999

[ZekeMarshall]

@editorialbot set v0.999 as version

Thanks @kthyng , sorry to be a bother, the version is now 0.9992, I had to make some corrections. The app has now been released to the public (https://www.ceh.ac.uk/data/software-models/modular-analysis-vegetation-information-system-mavis/rmavis) so this will be the last change before the review process. Thanks again!

[kthyng]

@editorialbot set v0.9992 as version

[editorialbot]

Done! version is now v0.9992

[kthyng]

This passed scope query!

@mikemahoney218 Would you like to edit this?

[kthyng]

@editorialbot invite @mikemahoney218 as editor

[editorialbot]

Invitation to edit this submission sent!

[mikemahoney218]

@editorialbot assign me as editor

Happy to take this one on! And I see that @ZekeMarshall has already listed suggested reviewers -- thanks for that, it's a huge help. I'll start pinging people for reviews today and tomorrow and will follow up as I hear back!

(And as a note to myself and to keep myself honest -- I just finished sending out the first round of invites)

[editorialbot]

Assigned! @mikemahoney218 is now the editor

[ZekeMarshall]

Hi @mikemahoney218 , thank you for accepting the role of editor and sending out reviewer invitations!

[mikemahoney218]

@editorialbot add adithirgis as reviewer

[editorialbot]

I can't add that reviewer: adithirgis is not a username

[mikemahoney218]

@editorialbot add @adithirgis as reviewer

[editorialbot]

@adithirgis added to the reviewers list!

[mikemahoney218]

@ZekeMarshall , would you be able to recommend any potential reviewers who have experience using GB NVC data in their research? I'm having a bit of a hard time finding anyone with a GitHub account who's worked with this data before, but think it's important that we get a review perspective from possible users of this tool as well as from R and Shiny experts -- if you can think of anyone from your network (so long as they don't have a conflict of interest) it would be a huge help. As before, please do not ping them using @ -- we'll only do that when we're actually inviting them :smile:

[ZekeMarshall]

Hi @mikemahoney218 , one potential reviewer would be Kevin Watts (watts-km) from Forest Research. I will ask my co-authors and get back to you about additional reviewers! Just to note RE conflicts of interest, I used to work at Forest Research, but in a different research group and never on any projects directly with Kevin. Thanks!

[ZekeMarshall]

Additional potential reviewers who are very experienced with vegetation ecology, but not necessarily the British NVC, and are active on Github could include:

• Jari Oksanen (jarioksa)
• Miquel De Cáceres (miquelcaceres)
• David Zelený (zdealveindy)

Another potential reviewer would be Maximilian Hesselbarth (mhesselbarth).

Thanks!

[ZekeMarshall]

@mikemahoney218 , a few suggestions from my co-authors for persons experienced with the British NVC, but who aren't necessarily active on Github could include:

• Ewan Mchenry (EwanMchenry@woodlandtrust.org.uk)
• Clare Pinches (Clare.Pinches@naturalengland.org.uk)
• Jamie Alison (jalison@ecos.au.dk)
• Roy Sanderson (roy.sanderson@newcastle.ac.uk)

Please let us know if you need any additional suggestions. Thanks again!