[REVIEW]: nsink: An R package for flow path nitrogen removal estimation

[whedon]

Submitting author: @jhollist (Jeffrey W Hollister)
Repository: https://github.com/USEPA/nsink
Branch with paper.md (empty if default branch):
Version: v1.2.0
Editor: @crvernon
Reviewers: @jmp75, @ldecicco-USGS, @jmp75
Archive: 10.5281/zenodo.6341565

⚠️ JOSS reduced service mode ⚠️

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Markdown: [![status](https://joss.theoj.org/papers/3af12dd8d27ca1605958d4fd021deaa8/status.svg)](https://joss.theoj.org/papers/3af12dd8d27ca1605958d4fd021deaa8)

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

@jmp75 & @ldecicco-USGS, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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✨ 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 ✨

Review checklist for @jmp75

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jhollist) 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

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 and who the target audience is?
• 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?

Review checklist for @ldecicco-USGS

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@jhollist) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @jmp75, @ldecicco-USGS it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1017

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.07 s (495.8 files/s, 65060.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            257            914           2179
Markdown                         5            101              0            349
TeX                              2             37              0            315
XML                              1              0              0            192
YAML                             3             25              2            121
Rmd                              2             70            239             54
-------------------------------------------------------------------------------
SUM:                            37            490           1155           3210
-------------------------------------------------------------------------------


Statistical information for the repository 'ad22c729492b33a55888e358' was
gathered on 2022/01/07.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.1016/j.ecoleng.2010.02.006 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v014.i06 is OK
- 10.1016/j.cageo.2004.03.012 is OK
- 10.32614/RJ-2016-014 is OK
- 10.1007/978-1-4614-7618-4 is OK
- 10.32614/RJ-2016-061 is OK
- 10.3133/ofr20191096 is OK
- 10.3390/rs11242971 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1641/0006-3568(2002)052[0129:BSIPGO]2.0.CO;2 is INVALID
- 10.32614/RJ-2021-048 is INVALID

[whedon]

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

[crvernon]

👋 @jhollist @jmp75 @ldecicco-USGS - the review takes place in this issue.

❗ Also, please don't forget to add a link to this review issue in any issues or pull requests you may generate in the https://github.com/USEPA/nsink repository. This will help everyone have a single point of reference.

[crvernon]

👋 @jmp75 and @ldecicco-USGS have you found that you are able to modify the user checklist above? Let me know if you have any further questions about how to conduct your review, etc. Thanks!

[ldecicco-USGS]

@jhollist should we be installing via the USEPA repo, or your fork? (I don't know if it matters, but the readme says your fork)
EDIT: I see the paper uses USEPA...

[jhollist]

@ldecicco-USGS sorry for the confusion, bit of a long story that I will spare you as to why I use the two...

It shouldn't matter. I have my local repo set to push to both locations so, in theory, they are identical. I use the EPA one in the paper and in DESCRIPTION so install from that. I do see now that I need to update my README installation instructions. Will do that shortly.

[ldecicco-USGS]

Say no more 😂

[ldecicco-USGS]

The package works as advertised, and the paper is clear to read. I don't see specific instructions on Community guidelines (I think this is generally a little different than the code of conduct that is included).

General thoughts, not required for approval, but might help some future developments:
The tests look to me to be written to check generally that the data coming back from the functions are set up in the intended structure and without errors. Since the package is heavily based on the Kellogg paper, it would be neat to see the tests recreate and match the results from the paper.

[crvernon]

📣 Mid-week rally!

👋 @jhollist - It looks like @ldecicco-USGS has requested a community guidelines section be added and has made several other helpful comments.

👋 @jmp75 - Were you able to initialize your review? Let me know if you have any questions.

Keep up the good work!

[jmp75]

@crvernon I am dragging the chain a bit, apologies. I'll allocate solid time over the coming two days.

[whedon]

👋 @ldecicco-USGS, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @jmp75, please update us on how your review is going (this is an automated reminder).

[jhollist]

@ldecicco-USGS and @crvernon thanks for the comments! There is a CONTRIBUTING.md but it is a little hidden inside of the .github folder. This is the defualt location for usethis::use_tidy_contributing which is what I used as an initial template for my contributing. This is one of the standard locations suggested by GitHub: https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/setting-guidelines-for-repository-contributors#adding-a-contributing-file. If JOSS has a different suggestion I am happy to move it.

Also, I will create an issue for a future enhancement that uses the Kellogg et al data for tests. This is a MOST excellent idea. Just will take some time to implement.

Thanks again!

[ldecicco-USGS]

Ack, sorry for not realizing that! Sure enough, it does make sense to put it in there.

[jhollist]

I will openly admit that I googled, "why is my contributing.md in the .github folder" prior to responding!

[crvernon]

@jmp75 - Please update me on the status of your review. Thanks!

[crvernon]

For record: I sent an email to @jmp75 today asking about the status of the review and the potential to conduct it.

[jmp75]

@crvernon I have gone through the checklist and I do not have other suggestions than that already provided by Laura.

I could not edit the checklist though, the link provided to validate it (accept the invitation) says it does not exist or not anymore, or a message to that effect.

[crvernon]

@whedon add @jmp75 as reviewer

[editorialbot]

Done! Archive is now 10.5281/zenodo.6341565

[crvernon]

@editorialbot set v1.2.0 as version

[editorialbot]

Done! version is now v1.2.0

[crvernon]

@jhollist - thanks for putting together a really nice software product! Thanks to @jmp75 and @ldecicco-USGS for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

[crvernon]

@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

- 10.1016/j.ecoleng.2010.02.006 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v014.i06 is OK
- 10.1016/j.cageo.2004.03.012 is OK
- 10.32614/RJ-2016-014 is OK
- 10.1007/978-1-4614-7618-4 is OK
- 10.32614/RJ-2021-048 is OK
- 10.32614/RJ-2016-061 is OK
- 10.3133/ofr20191096 is OK
- 10.3390/rs11242971 is OK

MISSING DOIs

- None

INVALID DOIs

- 10.1641/0006-3568(2002)052[0129BSIPGO]2.0.CO2 URL is INVALID

[crvernon]

NOTE: the invalid DOI resolves correctly per the author's comment:

The DOI for that reference is: 10.1641/0006-3568(2002)052[0129:BSIPGO]2.0.CO;2 and it resolves correctly at https://doi.org/10.1641/0006-3568(2002)052[0129:BSIPGO]2.0.CO;2. It appears that some of the special characters are getting lost. In the article proof, the square bracket are lost, but the URL resolves. As the DOI is correct in the .bib file, I am not sure what to do to get the JOSS DOI check to pass.

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3036

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3036, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[jhollist]

Thank you, @crvernon, @ldecicco-USGS, and @jmp75! JOSS is one of my favorite journals to submit to and review for!

[kyleniemeyer]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

🐦🐦🐦 👉 Tweet 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.04039 joss-papers#3045
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04039
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...

[kyleniemeyer]

Congratulations @jhollist on your article's publication in JOSS!

Many thanks to @jmp75 and @ldecicco-USGS for reviewing this, and @crvernon for editing.

[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.04039/status.svg)](https://doi.org/10.21105/joss.04039)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.04039">
  <img src="https://joss.theoj.org/papers/10.21105/joss.04039/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04039/status.svg
   :target: https://doi.org/10.21105/joss.04039

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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[editorialbot]

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

OK DOIs

- 10.1016/j.ecoleng.2010.02.006 is OK
- 10.1641/0006-3568(2002)052[0129:BSIPGO]2.0.CO;2 is OK
- 10.32614/RJ-2018-009 is OK
- 10.18637/jss.v014.i06 is OK
- 10.1016/j.cageo.2004.03.012 is OK
- 10.32614/RJ-2016-014 is OK
- 10.1007/978-1-4614-7618-4 is OK
- 10.32614/RJ-2021-048 is OK
- 10.32614/RJ-2016-061 is OK
- 10.3133/ofr20191096 is OK
- 10.3390/rs11242971 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[kthyng]

@crvernon Was this a mistake?

[crvernon]

@kthyng yes! sorry!