[REVIEW]: The sspm R package: spatial surplus production models for the management of northern shrimp fisheries #4724

editorialbot · 2022-09-01T15:09:02Z

Submitting author: @VLucet (Valentin Lucet)
Repository: https://github.com/pedersen-fisheries-lab/sspm
Branch with paper.md (empty if default branch): main
Version: v1.0.0
Editor: @Bisaloo
Reviewers: @quang-huynh, @kellijohnson-NOAA
Archive: 10.5281/zenodo.8015102

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/d05fcbbc7ff3d1d2bc3c56466f2e21e5/status.svg)](https://joss.theoj.org/papers/d05fcbbc7ff3d1d2bc3c56466f2e21e5)

Reviewers and authors:

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Reviewer instructions & questions

@quang-huynh & @kellijohnson-NOAA, 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

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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 ✨

Checklists

📝 Checklist for @quang-huynh

📝 Checklist for @kellijohnson-NOAA

The text was updated successfully, but these errors were encountered:

editorialbot · 2022-09-01T15:09:04Z

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 · 2022-09-01T15:09:07Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.05 s (1543.4 files/s, 218675.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               55           1767           2033           5118
TeX                              1             24              0            257
Markdown                         5             53              0            155
YAML                             6             28              7            136
Rmd                              3             81            143            116
-------------------------------------------------------------------------------
SUM:                            70           1953           2183           5782
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-09-01T15:09:08Z

Wordcount for paper.md is 1513

editorialbot · 2022-09-01T15:09:12Z

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

OK DOIs

- 10.1111/1365-2664.12664 is OK
- 10.1093/icesjms/fsz048 is OK
- 10.1093/icesjms/fsv229 is OK
- 10.1890/14-0739.1 is OK
- 10.1093/icesjms/fsw230 is OK
- 10.1111/j.1467-2979.2011.00452.x is OK
- 10.1146/annurev.ecolsys.39.110707.173406 is OK
- 10.1111/faf.12550 is OK
- 10.1139/F08-170 is OK
- 10.1139/f03-105 is OK
- 10.1890/14-0739.1 is OK
- 10.1111/j.1467-2979.2012.00488.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2022-09-01T15:11:17Z

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

Bisaloo · 2022-09-01T15:15:27Z

👋 👋 👋 @VLucet, @quang-huynh, @kellijohnson-NOAA this is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step 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#4724 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 let me know 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 feel free to ping me (@Bisaloo) if you have any questions/concerns.

quang-huynh · 2022-09-04T17:37:15Z

@editorialbot generate my checklist

Bisaloo · 2022-09-06T07:35:10Z

@quang-huynh, could you try re-running this command please? Something went wrong on our end.

quang-huynh · 2022-09-06T17:05:10Z

Review checklist for @quang-huynh

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/pedersen-fisheries-lab/sspm?
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 (@VLucet) 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?

quang-huynh · 2022-09-23T00:47:56Z

I reviewed the software by installing the package on my local desktop and going through the example in the An_example_with_simulated_data vignette. I was able to replicate the steps in the vignette on my R console and replicate the figures.

Documentation suggestions:

I noticed that many figures in the vignette are too small, so the figure width needs to be wider in the Rmarkdown document.

I also see that the smoothened density estimates (step 8) are identical in all four panels. Is this correct? Do P1-4 represent SFA?

The package is well organized for those familiar with S4 class system. I would recommend reducing the number of methods for generics whenever possible but this is not a major concern. For example, spm_as_dataset has 4 defined methods but two should suffice (for data.frame and sf).

Are model diagnostic tools available to evaluate goodness of fit? I see that sspm_model_fit@fit is a bam object with various methods already defined in the mgcv and stats packages. The vignette can be updated to indicate where the model object is located and what diagnostics are available.

A summary method for the sspm_fit S4 class would be very useful for reporting estimates of biomass and productivity (both by time/area), and all other outputs that would be important to advise management.

Functionality documentation The help documentation can be improved without much additional effort. For example, the help for spm_as_boundary says that the function creates a sspm_boundary object which is not helpful. The function divides polygons into smaller patches. An additional sentence to describe what these functions actually do should be added.

Community guidelines A quick statement in the README.md to recommending users to report bugs in Github issues will meet this requirement.

Paper suggestions:

State of the field There's not much reference to similar software. There are various software packages, e.g., spict, aspic, jabba, for surplus production models that estimate intrinsic rate of increase and carrying capacity. These model a unit stock without spatial considerations. However, sspm does not appear to estimate the inherent productivity of a population. Rather, sspm appears to use GAMs to estimate surplus production and productivity (C_y + B_y)/C_y-1 over space and time, as well as with any covariates provided to the model (I am not currently able to fully review the methodology underlying the package as I don't have access to the Pedersen et al. Res Doc).

In a fisheries context, sspm reminds me more of the VAST and sdmTMB packages that implement spatiotemporal GLMMs to predict response variables across a spatial field over time. It may be possible to somewhat replicate sspm in sdmTMB, but estimation in sspm will be much, much faster (compared to the use of Gaussian Markov random fields in the other packages), and sspm conveniently addresses a specific use-case for fisheries assessment. I recommend reference and comparison of these packages with sspm.

References The Pedersen et al and Prager reference needs to be edited to meet this requirement.

Other paper suggestions:

Line 13: Fisheries managers typically do not use analytical methods but receive advice from analysts. Perhaps "fisheries analysts" should be used instead of 'fisheries managers'?
Line 50: Suggest "Advice to managers advice should account for varying productivity"
Line 79: Should be "surplus production"

kellijohnson-NOAA · 2022-09-27T18:33:47Z

Review checklist for @kellijohnson-NOAA

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/pedersen-fisheries-lab/sspm?
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 (@VLucet) 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?

Bisaloo · 2022-11-11T17:10:33Z

Thanks a lot @kellijohnson-NOAA & @quang-huynh for your reviews!

@VLucet, do you have a timeline of when you could be able to address these comments?

VLucet · 2022-11-14T14:06:38Z

Thanks a lot to @kellijohnson-NOAA and @quang-huynh for your thoughtful reviews.
Yes, my apologies for the delay, these comments will be addressed by the end of ~~the month~~ the year.

VLucet · 2022-12-07T20:41:08Z

Hi all, my apologies for underestimating the amount of time it is taking me to address all the comments. I wanted to thank again @kellijohnson-NOAA and @quang-huynh for the detailed and helpful comments (the list of tasks they have given and the linked commits for addressing them are here: pedersen-fisheries-lab/sspm#54 and pedersen-fisheries-lab/sspm#59). All of @kellijohnson-NOAA's have been addressed.

@quang-huynh I also wanted to let you know that the research document is finally out here, in case there is more you wanted to add to your comment which mentions being unable to access it yet: pedersen-fisheries-lab/sspm#125)

quang-huynh · 2022-12-08T21:18:39Z

@VLucet Thanks for the link to the research document. The closest alternative to sspm appears to be VAST for spatial surplus production modeling: https://james-thorson-noaa.github.io/docs/tutorials/surplus-production/ The associated paper is https://doi.org/10.1111/1365-2664.12664 which the authors could use for comparison

The major benefit of sspm over VAST appears to be run time, the longer model runtime is VAST is associated with estimating the spatial random field. I've also found a big learning curve is needed with VAST. sspm addresses a much narrower use case which makes it easier to learn for a new user.

Bisaloo · 2023-01-20T06:42:32Z

Hi @VLucet, happy new year! Do you have an updated timeline of when you could go over the last remaining review comments? ☺️

VLucet · 2023-01-30T22:49:53Z

Hi @Bisaloo ! Happy new year as well. @eric-pedersen and I have been discussing how to address the last couple of comment relating to the text (pedersen-fisheries-lab/sspm#125 and pedersen-fisheries-lab/sspm#126). We need a little more time to finalize that. All the other comments and technical issues have been addressed in pedersen-fisheries-lab/sspm#58.

Bisaloo · 2023-03-01T21:00:18Z

Hi @VLucet, what is the status of your submission please? Do you have an estimated date where you aim at finalizing your updates. It would be great to not wait too much as to make sure your work is still fresh in the reviewer's memory.

Bisaloo · 2023-06-20T21:11:08Z

Thanks, I submitted one last PR (pedersen-fisheries-lab/sspm#144) to fix the format for co-first authors and everything is ready for acceptance after this!

VLucet · 2023-06-20T21:11:57Z

just saw, I merged it

Bisaloo · 2023-06-20T21:12:41Z

@editorialbot generate pdf

editorialbot · 2023-06-20T21:14:20Z

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

Bisaloo · 2023-06-20T21:17:11Z

@editorialbot recommend-accept

editorialbot · 2023-06-20T21:17:13Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-06-20T21:17:36Z

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

OK DOIs

- 10.1111/faf.12174 is OK
- 10.1016/j.fishres.2018.03.010 is OK
- 10.1111/faf.12398 is OK
- 10.1101/2022.03.24.485545 is OK
- 10.1016/j.fishres.2018.10.013 is OK
- 10.1111/1365-2664.12664 is OK
- 10.1093/icesjms/fsz048 is OK
- 10.1093/icesjms/fsv229 is OK
- 10.1890/14-0739.1 is OK
- 10.1093/icesjms/fsw230 is OK
- 10.1111/j.1467-2979.2011.00452.x is OK
- 10.1146/annurev.ecolsys.39.110707.173406 is OK
- 10.1111/faf.12550 is OK
- 10.1139/F08-170 is OK
- 10.1139/f03-105 is OK
- 10.1890/14-0739.1 is OK
- 10.1111/j.1467-2979.2012.00488.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-06-20T21:19:05Z

⚠️ Error preparing paper acceptance. The generated XML metadata file is invalid.

ID ref-thorson_importance_2015 already defined

VLucet · 2023-06-20T21:21:34Z

I see the error, the ref thorson_importance_2015 is defined twice. I'll fix it now.

VLucet · 2023-06-20T21:24:02Z

It should be fixed now.

Bisaloo · 2023-06-20T22:39:17Z

@editorialbot recommend-accept

editorialbot · 2023-06-20T22:39:18Z

Attempting dry run of processing paper acceptance...

editorialbot · 2023-06-20T22:39:32Z

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

OK DOIs

- 10.1111/faf.12174 is OK
- 10.1016/j.fishres.2018.03.010 is OK
- 10.1111/faf.12398 is OK
- 10.1101/2022.03.24.485545 is OK
- 10.1016/j.fishres.2018.10.013 is OK
- 10.1111/1365-2664.12664 is OK
- 10.1093/icesjms/fsz048 is OK
- 10.1093/icesjms/fsv229 is OK
- 10.1890/14-0739.1 is OK
- 10.1093/icesjms/fsw230 is OK
- 10.1111/j.1467-2979.2011.00452.x is OK
- 10.1146/annurev.ecolsys.39.110707.173406 is OK
- 10.1111/faf.12550 is OK
- 10.1139/F08-170 is OK
- 10.1139/f03-105 is OK
- 10.1111/j.1467-2979.2012.00488.x is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot · 2023-06-20T22:43:30Z

👋 @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#4328, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

VLucet · 2023-06-21T14:10:29Z

Looks good to me.

kthyng · 2023-06-21T18:49:49Z

Here is my to do list:

Check that version was updated
Check that software archive exists, has been input to JOSS, and title and author list look good
Check paper

kthyng · 2023-06-22T18:18:40Z

@editorialbot accept

editorialbot · 2023-06-22T18:18:41Z

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

editorialbot · 2023-06-22T18:20:24Z

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: Lucet
  given-names: Valentin
  orcid: "https://orcid.org/0000-0003-0268-818X"
- family-names: Pedersen
  given-names: Eric J.
  orcid: "https://orcid.org/0000-0003-1016-540X"
doi: 10.5281/zenodo.8015102
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Lucet
    given-names: Valentin
    orcid: "https://orcid.org/0000-0003-0268-818X"
  - family-names: Pedersen
    given-names: Eric J.
    orcid: "https://orcid.org/0000-0003-1016-540X"
  date-published: 2023-06-22
  doi: 10.21105/joss.04724
  issn: 2475-9066
  issue: 86
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 4724
  title: The sspm R package for spatially-explicit surplus production
    population models
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.04724"
  volume: 8
title: The sspm R package for spatially-explicit surplus production
  population models

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 · 2023-06-22T18:20:29Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot · 2023-06-22T18:20:29Z

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot · 2023-06-22T18:20:30Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.04724 joss-papers#4336
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04724
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Bisaloo · 2023-06-22T18:28:19Z

Congratulations @VLucet @eric-pedersen 🎉🎉!

Thanks a lot for your thorough and informative reviews @kellijohnson-NOAA @quang-huynh 🙏🙏!

VLucet · 2023-06-22T18:30:06Z

Yay! Thanks to you @Bisaloo as well!

kthyng · 2023-06-22T19:26:42Z

Congrats on your new publication @VLucet!! Many thanks to editor @Bisaloo and reviewers @quang-huynh and @kellijohnson-NOAA for your time, hard work, and expertise!!

editorialbot · 2023-06-22T19:26:44Z

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editorialbot added R review TeX labels Sep 1, 2022

editorialbot assigned Bisaloo Sep 1, 2022

editorialbot mentioned this issue Sep 1, 2022

[PRE REVIEW]: The sspm R package: spatial surplus production models for the management of northern shrimp fisheries #4497

Closed

editorialbot added the Track: 6 (ESE) Earth Sciences and Ecology label Sep 10, 2022

This was referenced Oct 3, 2022

No link in "see for more details" pedersen-fisheries-lab/sspm#53

Closed

Line-specific comments to 10.21105.joss.04724 pedersen-fisheries-lab/sspm#54

Closed

This was referenced Oct 5, 2022

Expand README pedersen-fisheries-lab/sspm#55

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Organize pkgdown reference index pedersen-fisheries-lab/sspm#56

Closed

Increase test coverage pedersen-fisheries-lab/sspm#57

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VLucet mentioned this issue Nov 20, 2022

JOSS Review pedersen-fisheries-lab/sspm#59

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13 tasks

editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jun 20, 2023

editorialbot added accepted published Papers published in JOSS labels Jun 22, 2023

kthyng closed this as completed Jun 22, 2023

[REVIEW]: The sspm R package: spatial surplus production models for the management of northern shrimp fisheries #4724

[REVIEW]: The sspm R package: spatial surplus production models for the management of northern shrimp fisheries #4724

Comments

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Reviewer instructions & questions

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Review checklist for @quang-huynh

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

quang-huynh commented Sep 23, 2022

kellijohnson-NOAA commented Sep 27, 2022 • edited Loading

Review checklist for @kellijohnson-NOAA

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Bisaloo commented Nov 11, 2022

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quang-huynh commented Dec 8, 2022

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VLucet commented Jun 21, 2023

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Bisaloo commented Jun 22, 2023

VLucet commented Jun 22, 2023

kthyng commented Jun 22, 2023

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quang-huynh commented Sep 6, 2022 •

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kellijohnson-NOAA commented Sep 27, 2022 •

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VLucet commented Nov 14, 2022 •

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