[REVIEW]: dia: An R package for the National Oceanic and Atmospheric Administration dam impact analysis

[editorialbot]

Submitting author: @danStich (Daniel Stich)
Repository: https://github.com/danStich/dia
Branch with paper.md (empty if default branch): main
Version: v1.0.1
Editor: @cheginit
Reviewers: @Fabbiologia, @rmk118
Archive: 10.5281/zenodo.14708353

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/7d2f12ac96edf4816423d178ad5731db/status.svg)](https://joss.theoj.org/papers/7d2f12ac96edf4816423d178ad5731db)

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

@Fabbiologia, 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 @cheginit 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 @rmk118

📝 Checklist for @Fabbiologia

[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:

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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]

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

✅ OK DOIs

- 10.25923/v67x-kk62 is OK
- 10.1525/bio.2009.59.11.7 is OK
- 10.3389/fmars.2021.734213 is OK
- 10.5281/zenodo.13376045 is OK
- 10.1093/icesjms/fsv083 is OK
- 10.1139/cjfas-2018-0008 is OK
- 10.1002/mcf2.10021 is OK
- 10.32614/CRAN.package.shiny is OK
- 10.32614/CRAN.package.ggplot2 is OK
- 10.21105/joss.01686 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Dam impact analysis model for Atlantic salmon in t...
- No DOI given, and none found for title: National Marine Fisheries Service Endangered Speci...
- No DOI given, and none found for title: R: A language and environment for statistical comp...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (841.4 files/s, 441784.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSS                              2              2             18          13339
R                               24            323           1720           1346
CSV                              3              0              0           1030
Markdown                         2             59              0            312
TeX                              1             12              0            131
YAML                             3             10              8             66
-------------------------------------------------------------------------------
SUM:                            35            406           1746          16224
-------------------------------------------------------------------------------

Commit count by author:

    79	danStich

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 825

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

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

[cheginit]

@editorialbot add @rmk118 as reviewer

[editorialbot]

@rmk118 added to the reviewers list!

[cheginit]

👋🏼 @danStich, @Fabbiologia, and @rmk118, this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step, as mentioned in the first comment of this issue, 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#7475 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 2-4 weeks. Please notify me if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please don't hesitate to ping me (@cheginit) if you have any questions/concerns.

[rmk118]

Review checklist for @rmk118

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/danStich/dia?
• 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 (@danStich) 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?

[rmk118]

Here is my initial review of the submission! If needed, I would be happy to open specific issues/PRs on the software repository for each point I mentioned below, but many of them are just minor points and I was not sure separate issues were warranted. I hope this is helpful, and let me know if you have any questions or concerns!

---

This submission provides an open-source tool to replace a previous Excel-based implementation of the DIA. As the Excel version has been mentioned in several scientific articles and federal reference documents, it seems likely that at a minimum, this package/paper will be cited by researchers who previously used the Excel model. The major limitation of this package is the extreme specificity to Atlantic salmon in the Penobscot River. While some of the helper functions (like make_eggs_per_female()) are relatively generalizable, arguments to the main package functions include parameters for specific dams on the Penobscot, and the package functionality is highly dependent on the built-in Penobscot River datasets. However, the Penobscot is a priority conservation area intensely studied by fisheries scientists, so there are still many researchers for whom this would be of interest. Furthermore, the relatively niche appeal of this package certainly does not mean it is not valuable– for example, the Excel-based DIA has been used to inform Federal Energy Regulatory Committee licensing activities at hydroelectric dams on the Penobscot. Having a powerful yet accessible open-source tool to support the transparency and reproducibility of the science behind federal management actions would be valuable even if it can only be used in specific scenarios.

General checks

• Substantial scholarly effort: As discussed in the paragraph above, this submission meets the scope eligibility described in the JOSS guidelines. However, I think it would be prudent to make it slightly more obvious that the project is currently only applicable to Penobscot River Atlantic salmon. For example, the Statement of Need section in the paper states “We created dia for use by fisheries researchers, managers, and practitioners interested in understanding population dynamics of intensively managed endangered Atlantic salmon in the USA.” The phrase “in the USA” is likely an overgeneralization of the package’s current functionality.

• Reproducibility: The figures in the paper could not be exactly reproduced without knowledge of the seed used for the random number generation. Similarly, I would recommend including set.seed() at the beginning of the README and help file examples to emphasize to users that otherwise results would not be reproducible. Also, when running the second README example I had to change it slightly in order to reproduce it on my computer: my laptop only has 8 cores, so I changed ncpus <- 10 to ncpus <- parallel::detectCores()-1.

Documentation

• A statement of need: The Overview section of the README could be expanded to be more explicit about “what problems the software is designed to solve and who the target audience is.”
• Functionality documentation: While the core functionality of the software is documented to a satisfactory level, I wanted to note that as someone who mainly uses future/furrr for parallelization, I had to reference the snowfall documentation to fully understand the parallel execution example in the README.
• Community guidelines: The package currently lacks “clear guidelines for third parties wishing to 1. contribute to the software 2. report issues or problems with the software 3. seek support.” Please provide these instructions in the README or within a dedicated CONTRIBUTING.md file linked in the README.

Software paper

• State of the field: It might be valuable to relate the functionality of this package to other software tools used for similar applications, especially the shadia package developed by the submitting author. In particular, emphasizing differences between the two packages besides the focal species could be useful for readers to quickly understand why DIA was developed as a separate project.
• Quality of writing: Please remove ‘Figure1’ from the image caption in the paper.md file, as “Figure 1” is automatically added before the caption when the file is rendered to a PDF. (Also note minor typo in the README: shownd instead of shown.)
• References:
  • Please ensure that in-text citations are correctly formatted. For example, “(e.g., @noaa:2013; @Nieland:2020)” renders as (e.g., National Marine Fisheries Service (2013); Nieland & Sheehan (2020)). Changing the markdown syntax to “[e.g., @noaa:2013; @Nieland:2020]” will remove the nested parentheses and hyperlink the entire citation instead of just the year, ensuring consistency with the in-text citations in the previous sentences.
  • Please update the year in the R Core Team citation from 2022 to 2024.
  • Please add a list of references to the README for the cited works (“Nieland et al. 2013, 2015; Nieland and Sheehan 2020”) and/or add hyperlinks to the relevant documents.

Other comments
I was wondering when it would be necessary to have stillwater_use_old included in the package?

[rmk118]

Hi @cheginit! @danStich did an excellent job addressing my comments about the package and paper, and I have now checked all of the boxes on my checklist. I think that my review is complete, and I would recommend this paper for publication. Let me know if there is anything else I need to do!

[cheginit]

@rmk118 Thank you for your timely time and effort in reviewing the submission and providing constructive comments! Appreciate it.

[cheginit]

👋🏼 @Fabbiologia, a friendly reminder for this review.

[Fabbiologia]

Review checklist for @Fabbiologia

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/danStich/dia?
• 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 (@danStich) 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?

[Fabbiologia]

👋🏼 @Fabbiologia, a friendly reminder for this review.

Very sorry for the delay, I will start now and plan to finish up in a week top

[cheginit]

@Fabbiologia Please start your review at your earliest convenient.

[editorialbot]

Done! archive is now 10.5281/zenodo.14708353

[cheginit]

@danStich Please use the same title as your JOSS submission for your Zenodo archive and add the two ORCIDs.

[danStich]

Thank you for noticing this. I changed the metadata in the Zenodo archive so the title matches the JOSS submission title and the correct creators are listed with ORCIDS for those who have them.

…

---- Daniel S. Stich (he/him) Associate Professor, Biology Department and Secretary-Treasurer, NY Chapter American Fisheries Society 113A Perna Science, SUNY Oneonta, NY 13820 Office: 607-436-3734 Cell: 518-860-4107 Email: ***@***.*** Website: danstich.github.io/stich<https://danstich.github.io/stich/index.html>

________________________________ From: Taher Chegini ***@***.***> Sent: Tuesday, January 21, 2025 9:46 AM To: openjournals/joss-reviews ***@***.***> Cc: Stich, Daniel ***@***.***>; Mention ***@***.***> Subject: Re: [openjournals/joss-reviews] [REVIEW]: dia: An R package for the National Oceanic and Atmospheric Administration dam impact analysis (Issue #7475) @danStich<https://github.com/danStich> Please use the same title as your JOSS submission for your Zenodo archive and add the two ORCIDs. — Reply to this email directly, view it on GitHub<#7475 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIYQJMIVJDSS3LCBYXRPJND2LZMUVAVCNFSM6AAAAABRWLJX7WVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMMBUHEZTINBTGQ>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[cheginit]

@editorialbot recommend-accept

Awesome, thank you!

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.25923/v67x-kk62 is OK
- 10.1525/bio.2009.59.11.7 is OK
- 10.3389/fmars.2021.734213 is OK
- 10.5281/zenodo.13376045 is OK
- 10.1093/icesjms/fsv083 is OK
- 10.1139/cjfas-2018-0008 is OK
- 10.1002/mcf2.10021 is OK
- 10.32614/CRAN.package.shiny is OK
- 10.32614/CRAN.package.ggplot2 is OK
- 10.21105/joss.01686 is OK
- 10.1093/icesjms/fsm012 is OK
- 10.5281/zenodo.597719 is OK
- 10.21105/joss.03444 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Dam impact analysis model for Atlantic salmon in t...
- No DOI given, and none found for title: National Marine Fisheries Service Endangered Speci...
- No DOI given, and none found for title: R: A language and environment for statistical comp...

❌ MISSING DOIs

- None

❌ 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#6353, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[cheginit]

I will now hand this over to EiC for final checks and publication. Meanwhile, please check the final proof in the previous comment to ensure the paper is correct.

@Fabbiologia, @rmk118 I'd like to thank for your time and effort in reviewing this submission and helping to improve the software, appreciate it!

@danStich, also, thank you for working diligently on addressing the comments and concerns of the reviewers and me!

[danStich]

I've reviewed the final proof and noted two typos: 1) an extra "of" in the second paragraph under "Statement of need" and an extra "the" in the third paragraph of the same section. I updated and pushed this correction to the repository.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[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]

Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file. I see "r" and "bayesian" and I think those should be capitalized but please check throughly for others.

[danStich]

Thank you. I checked all references and I noticed a couple other instances for R package names. It looks like these were references we added during review. New .bib file pushed to repository.

[kthyng]

@editorialbot generate pdf

[editorialbot]

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

[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: Stich
  given-names: Daniel S.
  orcid: "https://orcid.org/0000-0002-8946-1115"
- family-names: Nieland
  given-names: Julie L.
- family-names: Sheehan
  given-names: Timothy F.
  orcid: "https://orcid.org/0000-0002-9689-1180"
contact:
- family-names: Stich
  given-names: Daniel S.
  orcid: "https://orcid.org/0000-0002-8946-1115"
doi: 10.5281/zenodo.14708353
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Stich
    given-names: Daniel S.
    orcid: "https://orcid.org/0000-0002-8946-1115"
  - family-names: Nieland
    given-names: Julie L.
  - family-names: Sheehan
    given-names: Timothy F.
    orcid: "https://orcid.org/0000-0002-9689-1180"
  date-published: 2025-01-21
  doi: 10.21105/joss.07475
  issn: 2475-9066
  issue: 105
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 7475
  title: "dia: An R package for the National Oceanic and Atmospheric
    Administration dam impact analysis"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.07475"
  volume: 10
title: "dia: An R package for the National Oceanic and Atmospheric
  Administration dam impact analysis"

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]

🦋🦋🦋 👉 Bluesky post 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.07475 joss-papers#6355
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.07475
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...

[kthyng]

Congratulations on your new publication @danStich! Many thanks to editor @cheginit and to reviewers @Fabbiologia and @rmk118 for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Note we have a new tool for reviewers! You can go to https://joss.theoj.org/papers/reviewed_by/@your-github-username to see the JOSS submissions you have reviewed, and you can also copy a badge there with the number of your JOSS reviews.

@danStich If you'd like to join JOSS as a reviewer, please sign up at https://reviewers.joss.theoj.org/join!

[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.07475/status.svg)](https://doi.org/10.21105/joss.07475)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.07475">
  <img src="https://joss.theoj.org/papers/10.21105/joss.07475/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.07475/status.svg
   :target: https://doi.org/10.21105/joss.07475

This is how it will look in your documentation:

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