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

[editorialbot]

Submitting author: !--author-handle-->@danStich<!--end-author-handle-- (Daniel Stich) Repository: https://github.com/danStich/dia Branch with paper.md (empty if default branch): main Version: v1.0.0 Editor: !--editor-->@cheginit<!--end-editor-- Reviewers: @Fabbiologia, @rmk118 Archive: Pending

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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

[editorialbot]

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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]

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

[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

• [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/danStich/dia?
• [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 (@danStich) 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?

[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.