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

editorialbot commented 8 months ago

Submitting author: !--author-handle-->@equitable-equations@mikemahoney218<!--end-editor-- Reviewers: @ifoxfoot, @mhesselbarth Archive: 10.5281/zenodo.11002086

Status

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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 commented 8 months ago

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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot commented 8 months ago

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 commented 8 months ago

Wordcount for paper.md is 1065

editorialbot commented 8 months ago

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 commented 8 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 8 months ago

👋🏼 @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 commented 8 months ago

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

ifoxfoot commented 8 months ago

Review checklist for @ifoxfoot

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

mhesselbarth commented 8 months ago

Review checklist for @mhesselbarth

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

mikemahoney218 commented 8 months ago

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 commented 8 months ago

@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 commented 8 months ago

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

mikemahoney218 commented 8 months ago

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

ifoxfoot commented 8 months ago

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 commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 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 8 months ago

Awesome, thanks @ifoxfoot !

mikemahoney218 commented 8 months ago

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 commented 8 months ago

@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 commented 8 months ago

@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 commented 8 months ago

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 commented 8 months ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

mhesselbarth commented 8 months ago

@editorialbot set joss-revision as branch

editorialbot commented 8 months ago

Done! branch is now joss-revision

mhesselbarth commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:warning: An error happened when generating the pdf.

editorialbot commented 8 months ago

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

mhesselbarth commented 8 months ago

@editorialbot set joss-revision as branch @editorialbot generate pdf

editorialbot commented 8 months ago

Done! branch is now joss-revision

danielskatz commented 8 months ago

@mhesselbarth - FYI, @editorialbot only see the first line of a comment, so only one command per comment can work

mhesselbarth commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

:warning: An error happened when generating the pdf.

mhesselbarth commented 8 months ago

I finally started with the review and opened a few issues, mostly minor stuff - @equitable-equations et al. very nice packages!

@mikemahoney218 @danielskatz I was trying to rebuild the PDF from the joss-revision branch to work on top of @ifoxfoot comments and read the most recent version. Could you please assist given that there seems to be some error building

danielskatz commented 8 months ago

@editorialbot set joss_revision as branch

(underscore, not hyphen)

editorialbot commented 8 months ago

Done! branch is now joss_revision

danielskatz commented 8 months ago

@editorialbot generate pdf

mhesselbarth commented 8 months ago

Upsi 🙈 How embarrassing...Friday afternoon I guess. Thank you very much.

editorialbot commented 8 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 7 months ago

Thanks so much @mhesselbarth and @ifoxfoot for your reviews! @equitable-equations , please let us know on this issue once you've addressed the concerns raised by reviewers :smile:

equitable-equations commented 7 months ago

Thanks everyone for your patience. The API on which this package relies is currently failing in a way not anticipated by my tests (certain calls cause it to freeze with no error or even timeout). I've notified the developer and am working to update my test to account for this behavior. I'll respond to the rest of your suggestions as soon as this is resolved.

mikemahoney218 commented 7 months ago

@equitable-equations , do you have any status updates for us?

equitable-equations commented 7 months ago

@mikemahoney218 good timing. I'm pushing an update to CRAN shortly to address these new potential behaviors from the API. I have responses to other edit requests prepared and will post them for reviewers as soon as the new version is up.

equitable-equations commented 7 months ago

@ifoxfoot @mhesselbarth thanks again for your patience. This package has been updated to account for the unexpected API failures seen last month, changes which have been pushed to the main branch of the repo and which are now on CRAN. I believe i have responded to all of your suggestions and comments, which were both constructive and on-point. A new version of the paper reflecting all of this can be found in the joss revision branch.

mhesselbarth commented 7 months ago

Looks good to me. I now checked all boxes on the review list 👍

mikemahoney218 commented 7 months ago

Thank you so much @mhesselbarth -- and thanks for reviewing for JOSS (again)!

mikemahoney218 commented 6 months ago

@ifoxfoot , would you be able to look at the changes @equitable-equations has made, and let me know if the current state of the software addresses your initial concerns (or open new issues on the repository if you still have items you can't check on the checklist)?

ifoxfoot commented 6 months ago

@editorialbot generate pdf

editorialbot commented 6 months ago

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

ifoxfoot commented 6 months ago

Hi! I was able to look at all the issues and revisions and I feel that @equitable-equations has made improvements sufficient to check of all the requirements! Looks good!

mikemahoney218 commented 6 months ago

Thank you so much @ifoxfoot , and thank you for reviewing for JOSS!

@equitable-equations , I'll do my final checks and start the process for recommending acceptance tomorrow.

openjournals / joss-reviews