editorialbot commented 5 months ago

Submitting author: !--author-handle-->@ZekeMarshall@mikemahoney218<!--end-editor-- Reviewers: @adithirgis, @rasanderson Archive: 10.5281/zenodo.12627165

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/460c6f934a108fcf5a16d0f2ab77492e/status.svg)](https://joss.theoj.org/papers/460c6f934a108fcf5a16d0f2ab77492e)

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

📝 Checklist for @adithirgis

editorialbot commented 5 months ago

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editorialbot commented 5 months ago

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 commented 5 months ago

Paper file info:

📄 Wordcount for paper.md is 1179

✅ The paper includes a Statement of need section

editorialbot commented 5 months ago

License info:

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

editorialbot commented 5 months ago

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 commented 5 months ago

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

mikemahoney218 commented 5 months ago

👋🏼 @ZekeMarshall, @adithirgis, @rasanderson this is the review thread for the paper. Just about all of our communications will happen here from now on. :smile:

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 commented 5 months ago

Review checklist for @rasanderson

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/ZekeMarshall/RMAVIS/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 5 months ago

@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 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

@editorialbot generate pdf

editorialbot commented 5 months ago

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

ZekeMarshall commented 5 months ago

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 commented 5 months ago

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 commented 4 months ago

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 commented 4 months ago

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 commented 4 months ago

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

ZekeMarshall commented 4 months ago

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

editorialbot commented 4 months ago

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

ZekeMarshall commented 4 months ago

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?

rasanderson commented 4 months ago

Hi @mikemahoney218 and @ZekeMarshall I've now had a chance to look through the code, paper, and Shiny app., and think this is a really nice piece of work. I had a PhD student a couple of years ago doing lots of work on pseudoquadrats and MAVIS classifications (see Butler, 2020 Chapter 3 ) so this is very interesting to read. There has been a need for this sort of app and functionality for some time. Some general points:

The Shiny app

This worked well, both the online site hosted (presumably) by CEH, and the version built from the R code from the GitHub site. A number of relatively minor points:

I did wonder whether the 'landing page' was right. When the app starts, the user is greeted by the data input page. It actually took me a couple of minutes before I noticed the 'Documentation' tab at the top right. I'd recommend a separate landing page to the data input page, and that the land page is user-friendly, so that it is obvious that the data needs to be input / loaded, then options chosen etc.
Maybe change 'Documentation' to 'Help'.
On both my PCs, a centrally-managed Windows PC, and a Linux workstation, the Documentation comes up in a relatively small window rather than the full height of the screen. Not quite sure why this is, but possibly a 'FluidRow' shiny control needs modification in one of the R files, though I haven't managed to track it down.
Similarly, some of the 'popup' boxes have a close button, but this is a long way down, and you have to scroll down to find it. e.g. after clicking 'Validate survey data' a box headed 'Validate Survey Table Data' is displayed, and the background of the Shiny app becomes blurred. The Close button is not displayed, as it is off the bottom of the screen: I seemed to be doing a bit of random clicking before I found what was going on, and realised that I had to scroll down the full length of the screen.
How easy would it be to add other data upload format options? e.g. TurboVeg format, although I realise that as a commercial package this might not be compatible.
I ran some of the example datasets, generated outputs, downloaded reports, and these were all great.

Paper

This provides a good summary of the needs for the work, is clearly written and correctly referenced. Main queries are:

The paper (and Shiny app) is very UK-focussed, which to some extent is inevitable given its dependence on the National Vegetation Classification. JOSS is an international journal, however, so I think it's important to acknowledge a wider applicability of this type of method in countries other than the UK and Ireland. We had a similar NVC-based paper published a couple of years ago Butler & Sanderson, 2022 and reported examples from USA, Canada, Australia, NZ, European Vegetation Archive etc. to try and ensure that an international readership would still find the research relevant.
Both your paper and the Shiny app make use of pseudoquadrats, which I originally developed in collaboration with Steve Rushton and Nigel Critchley in the 1990s Sanderson et al 1995 Critchley et al 2002. However, the technique has never been widely adopted, and I suspect will be very unfamiliar to many readers, especially in an international audience. I'd therefore recommend that you expand your explanation of the pseudoquadrat concept, on both the Shiny app and in the paper, to ensure no ambiguity.
Use of Decorana (DCA). This is quite a controversial area: both TWINSPAN and DCA were the default multivariate classification and ordination systems respectively when the NVC was developed, but both have fallen out of favour since then. DCA has been criticised for sometimes over-correcting the 'arch' effect but then introducing a 'wedge' or 'triangle' effect in the display of points. You've used Oksanen's version of DCA, which will ensure that the results aren't sensitive to the input order of quadrats, which was a problem in the original version. However, in Numerical Ecology Legendre & Legendre 2012 they caution that '...MDS is the best technique for recovering complex gradients, not DCA', and '...detrending should be avoided, except for the specific purpose of estimating the lengths of gradients', but that 'satisfactory mathematical solutions to the problem of detrending remain to be found'. Of course, given the close association of the NVC with these methods, I think you're right to present DCA. However, I wonder whether you could modify the Shiny interface so that alternative MVA techniques could be offered to the end-user, such as NMDS, or PCA and its constrained equivalent, RDA etc? These are all very simple to implement in the R vegan package.

R code and Github site

Again, relatively minor comments.

The GitHub site could be improved. I think you need a much more thorough README.md file than the one currently provided. It's likely that quite a number of readers and / or eventual users would like more information on the GitHub site. When I am installing new software from GitHub, I much prefer a comprehensive README.md (even it some of its contents are repeated later, in the app), than a rather sparse one.
The R code is excellent, well-structured and organised, using Shiny modules to control the operation of the app, and lots of comments throughout.
Use of renv is a good idea. My Linux box automatically installed renv and prepared the R project correctly. My (centrally managed) Windows machine has an old version of RStudio (2022.12.0), and it failed to detect renv when I opened the R project file. You may therefore want to add instructions about installing renv, or specifiy a minimum version of RStudio for use with the app.
There isn't a formal API for this set of code, as it's an R project to drive a shiny app. However, to maximise takeup internationally, so that it can be used for other vegetation classifications not just the NVC, it needs to be easily customised. Having Shiny modules helps this. However, I notice all your R functions, for example in the six files in the R folder, are fully documented in the code. Once the project is loaded, it means that doing the usual ?habCor_data brings up the help information for that function. I'm wondering whether you've thought of making this a formal R package, as well as being a shiny app? This would expose the call, parameters, return values of these functions more explicitly. I'm not sure how complex it would be to create it as an R package hosted on GitHub (it doesn't need to go onto CRAN), but as an R library you'd then also have the possibility of a reference manual, package vignettes etc. Again, I'm thinking in terms of ensuring that what to me is an excellent tool has as wide an uptake as possible outside of the UK, by allowing end-users to easily customise parts of what you've created for their own shiny apps for their own regional vegetation classifications.

Enjoyed reading the research you've been doing - great stuff. Roy

mikemahoney218 commented 4 months ago

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

editorialbot commented 4 months ago

Done! repository is now https://github.com/NERC-CEH/RMAVIS

mikemahoney218 commented 4 months ago

Thank you so much for your review, @rasanderson !

ZekeMarshall commented 4 months ago

Hi @rasanderson ,

Thank you for your positive review!

In response to your comments:

The Shiny App

Good point about a landing page, I've added a landing page and rendered the README to this page.
Thanks for pointing out that the documentation opens in a small window, I've fixed the height to 85% of the screen, so it should scale for different monitors now.
I've added the ability to close the modal pop ups by clicking outside the window. Thanks for this suggestion.
This isn’t something we plan on adding at the moment, as we’re trying not to build out too much data wrangling functionality, rather leaving the user to do some work to get it into our simple 5 column format. But it is something that we could do in the future, especially given that packages such as {vegtable} already exist.

Paper

Thanks for pointing me in the direction of Butler & Sanderson (2022)! I did set up the app so that we could facilitate the incorporation of other vegetation classifications and taxonomic backbones in the future, as all underlying data are initialised as setup data in the setupData_server.R file. So I’m open to the idea, but for v1.0 I’d like to stick to the GB focus, perhaps building out this functionality for a future release.
Thanks for pointing me in the direction of Sanderson et al (1995) and Critchley et al (2002), I agree we should provide a better description, I’ve added these references to the documentation!
Good point RE the DCA. This is definitely something I thought/I’m currently thinking about, but not for v1.0 I think.

R code and Github site

Thanks for the suggestion, I've improved the README!
I’ll check out what the minimum RStudio version would be/is. However, I use Visual Studio Code and RStudio interchangeably so I also wouldn’t want to be too prescriptive about the choice of IDE. I have now instructed the user to install {renv} in the README.
I have structured the repo as a basic R package, which can be installed from Github with remotes::install_github(“NERC-CEH/RMAVIS”), and I use it in a few other projects now. So I will definitely be maintaining it as a package! As I mentioned before, the initial set up to generalise RMAVIS has been done in “setupData_server.R”, but I should also document the modules and export them as functions to facilitate re-use by others. This may not be for v1 though, as it would require more thought and building in the facility to turn off modules such as the MVA modules if no pre-calculated ordinations are available for the “National Reference” MVA; or when EIVs aren’t available etc, along with restructuring and renaming the bundled GB-specific data. So the bundled data and functions in /R are available via the RMAVIS ‘package’, but the shiny code is not yet!

Thanks again, the changes I've made above are contained in the latest release (v0.9998)!

Best regards,

Zeke

ZekeMarshall commented 4 months ago

@editorialbot generate pdf

editorialbot commented 4 months ago

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

rasanderson commented 4 months ago

Hi @ZekeMarshall and @mikemahoney218 Many thanks for making the suggested changes, to the shiny app, article and GitHub landing page. Everything looks good to me, so I'm now happy to sign off and approve. Roy

mikemahoney218 commented 4 months ago

Thank you so much for your review, @rasanderson !

@adithirgis , I wanted to bump this now that we're about a month into the review window, and ask how your review is progressing/if you're still expecting to complete your review on the original timeline.

Just as a reminder, the first step in the review is to post @editorialbot generate my checklist as the start of a new comment in this thread, which will generate a review checklist for you to use!

ZekeMarshall commented 4 months ago

Hi @rasanderson, thank you very much! Your review is really appreciated. All the best, Zeke

mikemahoney218 commented 4 months ago

@adithirgis , I wanted to reach back out to ask how things are progressing, and to see if you had any questions/comments about your review for JOSS!

Just as a reminder, the first step in the review is to post @editorialbot generate my checklist as the start of a new comment in this thread, which will generate a review checklist for you to use.

Thanks!

adithirgis commented 3 months ago

Hi, apologies for my tardiness. Will review soon.

Adithi

adithirgis commented 3 months ago

Review checklist for @adithirgis

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/NERC-CEH/RMAVIS?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

adithirgis commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

adithirgis commented 3 months ago

Hello @ZekeMarshall,

A great job on this software. A few minor points to share, please correct me if any points are already implemented -

Documentation

Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software - I think this needs to be separate document something like this - https://github.com/r-lib/usethis/blob/main/.github/CONTRIBUTING.md

Functionality

Installation: Does installation proceed as outlined in the documentation? - If I use the remotes::install_github("NERC-CEH/RMAVIS"); library(RMAVIS) what are the next steps to run the app. Please add it in the documentation. The other options works well.
I see that the online version uploaded here - https://connect-apps.ceh.ac.uk/RMAVIS/ works similar to the local version that is very well and smooth (the local version takes time to setup though), but I was thinking most of the data seems to be from UK. Since this app can be used in other
Also I recommend using devtools::check() - there are a few warnings and notes to consider.

Download report shows this error.

Warning in system2(..., stdout = if (use_file_stdout()) f1 else FALSE, stderr = f2) :
'"pdflatex"' not found
Warning: Error in : LaTeX failed to compile C:\Users\adith\AppData\Local\Temp\RtmpcNGUY2\file32643bc25352.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips.
1: shiny::runApp

Thank you, and apologies for the delay.

Adithi

ZekeMarshall commented 3 months ago

Hi @adithirgis ,

Thanks for your review!!

In response to your comments I have pushed a provisional v1.0 release to the v1 branch, this branch incorporates the following changes:

Added a function RMAVIS::runApp() to run RMAVIS after installation as a package.
Added instructions on how to run the RMAVIS app using the function above in the README.
Added instructions on how to install a LaTeX distribution to ensure the report can be generated (specifically using {tinytex}) in the README.
Included contributor guidelines.
Streamlined the dependencies.

In terms of the package checks, ensuring there are no warnings is a tricky job. The biggest issue is the presence of non-ASCII strings in the taxonomic backbone data. I need to think about the best way to handle this as I need to maintain compatibility with the taxonomic backbone source and convert these non-ASCII strings to ASCII for RMAVIS and check they are all correct. I would also like to do this following a major update to the United Kingdom Species Inventory later this year. @mikemahoney218 are you happy for me to leave this job for a future release?

Lastly, @adithirgis the only comment I'm unclear about is in the Functionality section of your review - "Since this app can be used in other". What do you mean by this?

Thanks again! Please let me know if my changes have addressed your comments. When everyone is happy I will then release the actual v1.0.

Best regards,

Zeke

ZekeMarshall commented 3 months ago

Hi @mikemahoney218 and @adithirgis , just to note that I will be from the office next week, so may be slow to reply!

mikemahoney218 commented 3 months ago

@adithirgis , have you had a chance to look at @ZekeMarshall 's response?

ZekeMarshall commented 3 months ago

Hi @mikemahoney218 & @adithirgis , I'm back from annual leave now. Please let me know if there any other changes you'd like me to make @adithirgis !

adithirgis commented 3 months ago

Hello,

Thank you for your response. I see that the changes are implemented. Regarding - "Since this app can be used in other" I meant in other countries as well.

Last question now that we need install.packages("tinytex") is it a required package in DESCRIPTION? Apologies I am confused regarding this step. Rest everything looks good! Good luck with the package.

Thanks, Adithi

ZekeMarshall commented 3 months ago

Hi @adithirgis ,

Thanks for your reply and checking the v1 branch!

I've added {tinytex} in the suggests (not the imports) section of the DESCRIPTION file as the user may already have a LaTeX distribution installed and so may not need {tinytex}. Thanks for pointing this out!

@mikemahoney218 , if you are ok with the reviews from @adithirgis and @rasanderson am I now ok to take the following steps for potential acceptance?

Merge v1 into main and release v1.0.0
Re-generate the article pdf

Cheers,

Zeke

mikemahoney218 commented 3 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[ ] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[ ] Check that the archive title, author list, version tag, and the license are correct
[ ] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

mikemahoney218 commented 3 months ago

Thank you so much @rasanderson and @adithirgis for your thoughtful reviews here.

@ZekeMarshall, at this point could you follow the checklist in the above message (and yes, merge & release 1.0.0)? I can then move forward with recommending acceptance of the submission.

As a general note -- I'm generally offline this week for a holiday, so might be slow to respond to this issue. I'll be back next week and only intermittently online until then.

ZekeMarshall commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

ZekeMarshall commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

openjournals / joss-reviews

[REVIEW]: RMAVIS v1.0: a Shiny application for the analysis of vegetation survey data and assignment to GB NVC communities #6682

Status

Reviewer instructions & questions

Checklists

Review checklist for @rasanderson

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

The Shiny app

Paper

R code and Github site

Review checklist for @adithirgis

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Documentation

Functionality

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance