[PRE 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: v1.0.0
Editor: @cheginit
Reviewers: @Fabbiologia
Managing EiC: Kristen Thyng

Status

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

Author instructions

Thanks for submitting your paper to JOSS @danStich. Currently, there isn't a JOSS editor assigned to your paper.

@danStich if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (815.5 files/s, 428018.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSS                              2              2             18          13339
R                               24            323           1720           1346
CSV                              3              0              0           1030
Markdown                         2             58              0            311
TeX                              1             12              0            128
YAML                             3             10              8             66
-------------------------------------------------------------------------------
SUM:                            35            405           1746          16220
-------------------------------------------------------------------------------

Commit count by author:

    69	danStich

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 769

✅ The paper includes a Statement of need section

[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
- 10.1093/icesjms/fsv083 is OK
- 10.1139/cjfas-2018-0008 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: dia: Atlantic salmon dam impact analysis (DIA) for...
- No DOI given, and none found for title: shiny: Web application framework for R
- No DOI given, and none found for title: R: A language and environment for statistical comp...
- No DOI given, and none found for title: ggplot2: Elegant graphics for data analysis

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1002/mcf2.10021 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

License info:

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

[editorialbot]

⚠️ An error happened when generating the pdf. Problem with affiliations for Julie Nieland, perhaps the affiliations index need quoting?.

[kthyng]

👋 @danStich - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it.

[danStich]

@editorialbot generate pdf

I think it may have been an un-indented "index" tag but I quoted the affiliations just in case (they were all single). Checking here.

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danStich]

Hi @kthyng,
I think the changes fixed the compilation problem.

[kthyng]

Hi @danStich and thanks for your submission! I am looking for some specific items to make sure your submission fits our requirements at a high level (not at the more detailed review level) before moving on to finding an editor or putting this on our waitlist if no relevant editors are available. I'll comment over time as I have a chance to go through them:

• OSI-approved license
• Installation instructions
• Documentation exists at all
• Tests of some sort
• Check paper (make sure compiles, read through, check for length 250-1000 words)
• Substantial scholarly effort
• Clear research application

In the meantime, please take a look at the comments above ⬆️ from the editorialbot to address any DOI, license, or paper issues if you're able (there may not be any), or suggest reviewers. For reviewers, please suggest 5 reviewers from the database listed above or your own (non-conflicted) extended network. Their github handles are most useful to receive but please don't use "@" to reference them since it will prematurely ping them.

[danStich]

Sounds great, thank you. I can find the 'skipped' DOIs from the reference check in the meantime and start putting together a list of potential reviewers.

[kthyng]

@danStich This looks ready to go though an example plot in your docs would be great — something to look at, a little more of a tutorial sort of thing. Just a suggestion.
We have a backlog of submissions so I will add this to our waitlist. Thanks for your patience.

[danStich]

@kthyng Thank you, I can add an example plot. I think we may have had one in an earlier internal draft as well. I have another MS in revision that has a short turnaround time so it may be Monday before I address the items I added for myself to the list below.

• Skip DOIs
  All but three of these were resolved. NOAA (2013), Nieland et al. (2013), and R Core Team (2022) did not have DOIs.
• example plot
• 5 Reviewers from database listed above or extended, non-conflicted network:

Potential Reviewers

From the JOSS reviewer database from most similar to least based on tags and profiles:

• Ruby Kasnow (rmk118): Experience with R, fisheries analyses, and dynamic simulation modeling listed in reviewer profile
• Kathryn Doering (k-doering-noaa): Experience with R and Fisheries Ecology listed in reviewer profile
• fabbiologia: Experience with R, Ecology, Fisheries, and Conservation listed in reviewer profile
• hvoltbb: Experience with R, Ecology, Fisheries, and Conservation listed in reviewer profile

From the 5 most similar JOSS submissions listed for this submission:

• Pasquale Buonomo (Shyentist): Authored JOSS paper about fisheries analysis tools for R

From extended, non-conflicted network

• Richard (Richie) Erickson (rerickson-usgs): Former co-author, experience with fisheries analyses in R reproducible research, authoring R packages
• Doug Sigourney (dsigourn): Former co-author, experience with fisheries analyses in R, familiarity with NOAA Dam Impact Analysis

[danStich]

@editorialbot generate pdf

Checking that PDF compiles following updated DOIs and addition of example figure (Figure 1).

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

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Submitting author: @mcsiple
Handling editor: @fboehm (Active)
Reviewers: @ha0ye, @tbrown122387
Similarity score: 0.7205

Reference Point Calculator (RPC): A Shiny app for exploration of limit reference points for fisheries management
Submitting author: @quang-huynh
Handling editor: @graciellehigino (Retired)
Reviewers: @ivnols, @katherinehebert
Similarity score: 0.7165

stacomiR : a common tool for monitoring fish migration
Submitting author: @MarionLegrandLogrami
Handling editor: @arfon (Active)
Reviewers: @steffilazerte, @boshek
Similarity score: 0.7094

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Handling editor: @graciellehigino (Retired)
Reviewers: @TanyaS08, @salix-d
Similarity score: 0.7041

nsink: An R package for flow path nitrogen removal estimation
Submitting author: @jhollist
Handling editor: @crvernon (Active)
Reviewers: @jmp75, @ldecicco-USGS, @jmp75
Similarity score: 0.7031

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[kthyng]

@cheginit Could you edit this submission?

[kthyng]

@editorialbot invite @cheginit as editor

[editorialbot]

Invitation to edit this submission sent!

[cheginit]

@kthyng Yes, I can edit this.

[cheginit]

@editorialbot assign @cheginit as editor

[editorialbot]

Assigned! @cheginit is now the editor

[cheginit]

👋🏼 @rmk118, @Fabbiologia, and @k-doering-NOAA, Would you like to review this submission to the Journal for Open Source Software? Our reviews are checklist-driven and openly conducted on GitHub over a timeline of 4–6 weeks. Because the process is much more iterative and interactive than a traditional paper review, we would ask you to start within the next 2 weeks. Here are reviewer guidelines for reference: joss.readthedocs.io/en/latest/reviewer_guidelines.html

Thanks for your consideration.

[rmk118]

Hi @cheginit! I would be happy to edit this submission. This will be my first JOSS review, so I apologize in advance if I am not the smoothest at navigating the logistics of reviewing on GitHub.

[cheginit]

@rmk118 Thanks for agreeing to review this submission and welcome to the JOSS community! I will provide detailed instructions for the review, and you can also read JOSS's guideline for more information.

Once I find another reviewer, I will open a new issue and ping you with instructions to being the review. Thanks!

[Fabbiologia]

hi @cheginit sorry for the delay, I was on the field. Will be happy to review this work.

[editorialbot]

Checklists can only be created once the review has started in the review issue

[cheginit]

@Fabbiologia Thanks for agreeing to review this submission! I will open a new issue with instructions to being the review.

[cheginit]

@editorialbot add @Fabbiologia as reviewer

[editorialbot]

@Fabbiologia added to the reviewers list!

[cheginit]

@editorialbot start review

[editorialbot]

OK, I've started the review over in #7475.