[REVIEW]: The fqar package: R tools for analyzing floristic quality assessment data

[editorialbot]

Submitting author: @equitable-equations (Andrew Gard)
Repository: https://github.com/equitable-equations/fqar
Branch with paper.md (empty if default branch): joss_revision
Version: v0.5.3
Editor: @mikemahoney218
Reviewers: @ifoxfoot, @mhesselbarth
Archive: 10.5281/zenodo.11002086

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7f3485f770c22ba09f37f74036d8ecd9/status.svg)](https://joss.theoj.org/papers/7f3485f770c22ba09f37f74036d8ecd9)

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

@ifoxfoot & @mhesselbarth, 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 @ifoxfoot

📝 Checklist for @mhesselbarth

[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=0.20 s (497.2 files/s, 34111.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               88            839           1487           2876
HTML                             1             84              5            549
Markdown                         5            117              0            215
TeX                              1             24              4            181
YAML                             2             11              6             55
Rmd                              1             67            161             43
-------------------------------------------------------------------------------
SUM:                            98           1142           1663           3919
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 1065

[editorialbot]

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

OK DOIs

- 10.18637/jss.v059.i10 is OK

MISSING DOIs

- 10.1016/j.ecolind.2014.11.017 may be a valid DOI for title: A null model test of Floristic Quality Assessment: Are plant species’ Coefficients of Conservatism valid?
- 10.1672/0277-5212(2006)26[718:papotf]2.0.co;2 may be a valid DOI for title: Properties and performance of the floristic quality index in Great Lakes coastal wetlands
- 10.3375/0885-8608(2006)26[17:tteosr]2.0.co;2 may be a valid DOI for title: Testing the efficacy of species richness and floristic quality assessment of quality, temporal change, and fire effects in tallgrass prairie natural areas
- 10.1093/aobpla/plx073 may be a valid DOI for title: Ecology of Floristic Quality Assessment: testing for correlations between coefficients of conservatism, species traits and mycorrhizal responsiveness
- 10.1016/j.ecolind.2020.107078 may be a valid DOI for title: Niche ecology in Floristic Quality Assessment: Are species with higher conservatism more specialized?
- 10.1002/ecs2.2825 may be a valid DOI for title: Floristic Quality Assessment: a critique, a defense, and a primer

INVALID DOIs

- None

[editorialbot]

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

[mikemahoney218]

👋🏼 @equitable-equations, @ifoxfoot, @mhesselbarth : 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. 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#6366 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. Thanks again so much for agreeing to review!

[equitable-equations]

@ifoxfoot & @mhesselbarth thanks to the reviewers for your work! I'll respond to questions or pull requests as promptly as I'm able.

[ifoxfoot]

Review checklist for @ifoxfoot

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/equitable-equations/fqar?
• 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 (@equitable-equations) 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?

[mhesselbarth]

Review checklist for @mhesselbarth

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/equitable-equations/fqar?
• 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 (@equitable-equations) 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]

Hi folks! Just wanted to bump this thread now that we're about two weeks into the review window -- thank you so much @ifoxfoot and @mhesselbarth for generating your review checklists, and please let me know if you have any questions/comments/concerns during your review!

[equitable-equations]

@mikemahoney218 I already have paper revision requests and suggestions from @ifoxfoot which I'm in the process of implementing or otherwise addressing. My thanks to all concerned!

[mhesselbarth]

I was sick, so need a couple of more days. Sorry for the delay.

[mikemahoney218]

Thanks for keeping us updated @mhesselbarth , hope you're feeling better!

[ifoxfoot]

hi @mikemahoney218 I plan on going through the documentation and reading @equitable-equations's updates to the manuscript today! I should be finished with the checklist in a couple of days max!

[ifoxfoot]

@editorialbot generate pdf

[editorialbot]

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

[mikemahoney218]

Awesome, thanks @ifoxfoot !

[mikemahoney218]

Also, looking at the paper preview, I think that any changes @equitable-equations makes won't be reflected in the preview until they get merged into the joss branch. As a result, I think the above preview reflects the original submission, and not the joss_revisions branch. Just want to make sure there's no confusion why changes aren't being reflected!

[equitable-equations]

@mikemahoney218 that's right. I wasn't sure about standard practice on this so I made a new temporary branch while others are still working. The changes are small, but if anyone wants to see the updated version directly you can do so here.

[ifoxfoot]

@mikemahoney218 and @equitable-equations okay thanks! That makes sense.

I do have one question for @mikemahoney218. Both the documentation and the software paper sections have checklist items for a statement of need. Is it necessary to have a statement of need in two places? Or is one statement of need in the paper sufficient to check both items off? Thanks!

[mikemahoney218]

We're generally looking for a statement of need in both the paper and the documentation. The main idea is that most users (and other people encountering the project) are probably going to find the documentation before the paper, and it's useful to give them a sense of what your project does and why. That can make it a lot easier to understand the intended use cases for a project and onboard new users.

That said, this section doesn't need to be as formal as it would be in the paper -- to use an example from one of my own projects, I generally include a "Why do this?" in the Readme:
https://github.com/ropensci/unifir?tab=readme-ov-file#why-do-this

[editorialbot]

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

[mikemahoney218]

@equitable-equations , would you be willing to update the Zenodo archive to list the paper co-authors as co-authors on the release, rather than "project members"? Or, do you have a reason that they shouldn't be listed as authors on this archive? I think this is the last thing outstanding before I can go ahead and recommend acceptance, and hand this back to the EiC for final processing.

[equitable-equations]

@mikemahoney218 done. This was just awkwardness from my first time using Zenodo. Thanks once more for all your work!

[mikemahoney218]

@editorialbot set 10.5281/zenodo.11002086 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11002086

[mikemahoney218]

@editorialbot set v0.5.3 as version

[editorialbot]

Done! version is now v0.5.3

[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

- 10.18637/jss.v059.i10 is OK
- 10.1016/j.ecolind.2014.11.017 is OK
- 10.1672/0277-5212(2006)26[718:papotf]2.0.co;2 is OK
- 10.3375/0885-8608(2006)26[17:tteosr]2.0.co;2 is OK
- 10.1093/aobpla/plx073 is OK
- 10.1016/j.ecolind.2020.107078 is OK
- 10.1002/ecs2.2825 is OK
- 10.1002/ecs2.2825 is OK

MISSING DOIs

- No DOI given, and none found for title: fqadata: Contains Regional Floristic Quality Asses...
- No DOI given, and none found for title: fqacalc: Calculate Floristic Quality Assessment Me...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Flora of the Chicago Region: A Floristic and Ecolo...
- No DOI given, and none found for title: Plants of the Chicago region

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#5268, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[mikemahoney218]

🎉 With everything looking good on my end, it's time for me to hand this back to the EiC for last steps. Thanks @equitable-equations for the submission, and thank you so much to @ifoxfoot and @mhesselbarth for reviewing!

[kthyng]

Hi! I'll take over now as Track Associate Editor in Chief to do some final submission editing checks. After these checks are complete, I will publish your submission!

• Are checklists all checked off?
• Check that version was updated and make sure the version from JOSS matches github and Zenodo.
• Check that software archive exists, has been input to JOSS, and title and author list match JOSS paper (or purposefully do not).
• Check paper.

[kthyng]

Everything looks great!

[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: Gard
  given-names: Andrew
  orcid: "https://orcid.org/0000-0003-4434-0755"
- family-names: Myers
  given-names: Alexia
- family-names: Luwabelwa
  given-names: Irene
contact:
- family-names: Gard
  given-names: Andrew
  orcid: "https://orcid.org/0000-0003-4434-0755"
doi: 10.5281/zenodo.11002086
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Gard
    given-names: Andrew
    orcid: "https://orcid.org/0000-0003-4434-0755"
  - family-names: Myers
    given-names: Alexia
  - family-names: Luwabelwa
    given-names: Irene
  date-published: 2024-04-23
  doi: 10.21105/joss.06366
  issn: 2475-9066
  issue: 96
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6366
  title: "The fqar package: R tools for analyzing floristic quality
    assessment data"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06366"
  volume: 9
title: "The fqar package: R tools for analyzing floristic quality
  assessment data"

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.06366 joss-papers#5270
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06366
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...

[equitable-equations]

Woohoo! Thanks @kthyng for your work!

[kthyng]

Congratulations on your new publication @equitable-equations! Many thanks to @mikemahoney218 and to reviewers @ifoxfoot and @mhesselbarth for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

[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.06366/status.svg)](https://doi.org/10.21105/joss.06366)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06366">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06366/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06366/status.svg
   :target: https://doi.org/10.21105/joss.06366

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:

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