[PRE REVIEW]: SAMPL: An agent-based model to evaluate spatial sampling strategies

[editorialbot]

Submitting author: @ifoxfoot (Iris Foxfoot)
Repository: https://github.com/EcoModTeam/SAMPL
Branch with paper.md (empty if default branch):
Version: 1.0.0
Editor: Pending
Reviewers: Pending
Managing EiC: Kristen Thyng

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/dd72b944eeb3d50c50b798a84333d7e6"><img src="https://joss.theoj.org/papers/dd72b944eeb3d50c50b798a84333d7e6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/dd72b944eeb3d50c50b798a84333d7e6/status.svg)](https://joss.theoj.org/papers/dd72b944eeb3d50c50b798a84333d7e6)

Author instructions

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

@ifoxfoot 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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:

@editorialbot commands

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

@editorialbot generate pdf

[editorialbot]

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

✅ OK DOIs

- 10.1111/j.1600-0587.2010.06421.x is OK
- 10.1111/j.1365-2664.2008.01545.x is OK
- 10.1890/14-1826.1 is OK
- 10.1899/04-138.1 is OK
- 10.1007/s10750-019-04017-y is OK
- 10.1080/01621459.1990.10474975 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: ArcGIS Pro
- No DOI given, and none found for title: NetLogo

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (627.6 files/s, 31881.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TeX                              1              9              0            104
Markdown                         2             35              0             75
YAML                             1              1              4             25
CSV                              1              0              0              1
-------------------------------------------------------------------------------
SUM:                             5             45              4            205
-------------------------------------------------------------------------------

Commit count by author:

    22	ifoxfoot
     6	Iris Foxfoot
     1	Kiara Cushway
     1	TSwan
     1	cushkia1

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 843

✅ 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 📄 👈

[editorialbot]

Five most similar historical JOSS papers:

fishStan: Hierarchical Bayesian models for fisheries
Submitting author: @rerickson-usgs
Handling editor: @marcosvital (Active)
Reviewers: @MikeKaller, @Cole-Monnahan-NOAA
Similarity score: 0.7075

portalcasting: Supporting automated forecasting of rodent populations
Submitting author: @gmyenni
Handling editor: @marcosvital (Active)
Reviewers: @ViniciusBRodrigues, @FlukeAndFeather
Similarity score: 0.7006

Cacatoo: building, exploring, and sharing spatially structured models of biological systems
Submitting author: @bramvandijk88
Handling editor: @Bisaloo (Retired)
Reviewers: @emilydolson, @TimKam
Similarity score: 0.6906

FielDHub: A Shiny App for Design of Experiments in Life Sciences
Submitting author: @DidierMurilloF
Handling editor: @csoneson (Active)
Reviewers: @Prof-ThiagoOliveira, @dlebauer
Similarity score: 0.6867

SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models
Submitting author: @k-doering-NOAA
Handling editor: @sbenthall (Active)
Reviewers: @quang-huynh, @iagomosqueira
Similarity score: 0.6866

⚠️ 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]

@ifoxfoot Hi! I don't see any code — where is your software repository?

[ifoxfoot]

@kthyng Hi! It is in the repository here https://github.com/EcoModTeam/SAMPL. The code is in the file called SAMPL.nlogo. Let me know if it's not showing up for you!

[ifoxfoot]

@kthyng re suggested reviewers. It looks like there is one published JOSS paper that is about a NetLogo model. I would recommend the authors of this paper https://joss.theoj.org/papers/10.21105/joss.05731 as reviewers.

[kthyng]

Hi @ifoxfoot 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.

Ok this will be tricky to find reviewers for this sort of niche paper – please dig deep for more reviewer suggestions if you can!

[kthyng]

@ifoxfoot comments/questions:

• I'm looking for docs for your software. I see this in your readme "For more information consult the model documentation, located in the Info tab of the NetLogo model." How do I do that? I'm looking for docs that a potential user of your software could browse to see if they want to use it.
• Are there tests so a user can verify the software is working correctly once they have it installed?
• We don't have a lot of netlogo reviewers in our database, so please suggest more reviewers who are not conflicted with you or your coauthors to suggest. This will probably be tricky to find enough to review.

[ifoxfoot]

hi @kthyng, thanks for the questions!

1. If the user has NetLogo installed and they download our model or clone it from GitHub, it would look like this:
   
   the info tab where the model documentation is located in is circled in red. Without downloading the file and opening it via NetLogo, viewing the user documentation is more tricky...but it can be seen on lines 1448-1530 of the SAMPL.nlogo file. I could also copy the documentation into a separate file if needed :)
2. There aren't automated tests but, once the model is downloaded, the user will be able to see a graphical user interface. They can then visually check that what the model is showing matches the inputs.
3. For reviewers, I'm reaching out to people who I think would be a good fit, but I don't have their GitHub user names yet. In the mean time I would suggest platipodium, Fabbiologia, nick-gauthier, and changliao1025 based off of previous JOSS authorship and reviews. Also agerada from the JOSS reviewer database. I also recommend jzkelter, nicolaspayette and bainco, based on their GitHub contribution history. Also I am familiar with the work of mwrossi who would be a great reviewer. I will add more soon, thanks!

[kthyng]

I'm going to ping the editorial board to take a look at this submission to see if it is in scope for JOSS in terms of substantial scholarly effort. This will take a few weeks — takes for your patience.

For reference, running cloc when it recognizes NetLogo gives this:

[kthyng]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[ifoxfoot]

@kthyng thanks! re substantial scholarly effort, commit history is rather lacking because the model was previously in a private repository on one of the author's profiles. We opted to make a fresh repository in a GitHub organization....so the early commits aren't shown.

[ifoxfoot]

@kthyng any updates on the editorial review? Thanks!

[kthyng]

@ifoxfoot Thank you for the ping, I will push on my end.

[kthyng]

@ifoxfoot Can you answer a couple of questions to help with this process?

• Since we can't see the full commit history, can you tell us about how long it has been?
• None of us are familiar with Netlogo. Can you give us a feel for about how much of the code is boilerplate (say, to handle buttons and user interface) vs the code that you wrote that you would consider to be your contribution in this package?
• You referenced one ArcGIS tool as having similar functions, but a quick google search revealed a whole book on spatial sampling in R: https://dickbrus.github.io/SpatialSamplingwithR/. Can you speak to if there are many more tools with this sort of functionality or if there are attributes that make this tool unusual in your subdiscipline?

[ifoxfoot]

Hi @kthyng yes!

• My team met every other week for about 10 months. We spent a lot of time discussing the theory behind the code rather than the code itself (although we did do that too). Mostly we tried to figure out how surveyors behave, how long they spend searching a quadrat, what distributions mussels/target species would be in, etc.
• The code is from lines 0-941. The rest is boilerplate for the interface and documentation that we wrote.
• Thanks for bringing up the R spatial sampling book, we can certainly reference it. There are a couple of things that make our tool stand out.

1. We chose NetLogo because it is easy to develop a user interface. While you can analyze or develop spatial sampling protocols in R, you would have to build your simulations and visualizations with code. With SAMPL, the sampling methodology and target species are all built in and users can interact with them using a point and click interface. Also, NetLogo can be rendered as html and hosted online, which is something we plan on doing.
2. SAMPL has a timed search feature that simulates human searching behavior. We haven't found any other tools that do this.

[ifoxfoot]

Hey @kthyng, I'm checking back in. Any updates? Are there any other questions I can answer to help the JOSS team make a scoping decision? Thanks!

[kthyng]

Hi @ifoxfoot, sorry for my delay. Unfortunately the editorial board has determined this submission to be out of scope. The information you provided was helpful, and the software looks really useful, making this a difficult decision. Ultimately, it came down to the fact that strictly GUI code like this is something we typically can't review well. It's not easily tested and it isn't designed for maintainable extension, which is a requirement for software we review.

Here is some information for publishing your software other ways if you're interested: https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages

Thanks for your interest in JOSS.

[kthyng]

@editorialbot reject

[editorialbot]

Paper rejected.

[ifoxfoot]

Hi @kthyng, I understand! Thank you for your time and consideration.