[REVIEW]: SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models

[editorialbot]

Submitting author: !--author-handle-->@k-doering-NOAA<!--end-author-handle-- (Kathryn Doering) Repository: https://github.com/nmfs-fish-tools/ssmse Branch with paper.md (empty if default branch): Version: v0.2.8 Editor: !--editor-->@sbenthall<!--end-editor-- Reviewers: @quang-huynh, @iagomosqueira Archive: 10.5281/zenodo.10014307

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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

@seananderson & @quang-huynh, 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 @sbenthall 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 @seananderson

📝 Checklist for @quang-huynh

📝 Checklist for @iagomosqueira

[editorialbot]

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

[k-doering-NOAA]

@quang-huynh I realized the changes we made were in a branch, rather than in the main branch, from which the paper draft was being built. I just went and merged the changes into the main branch and rebuilt the paper - see the above editorialbot comment that should include the changes to the draft. I hope this helps!

[quang-huynh]

Thanks @k-doering-NOAA

The updates are suitable for me and I've checked off the outstanding items.

Some minor comments:

Functionality documentation Projected dynamics in the operating model can be tinkered with a list, with a template provided by SSMSE::create_future_om_list. However, there's no documentation in the help file on what information is needed and what options are possible. What are the required values for 'pars', 'scen', 'pattern', and 'input' entries in the list? I can figure it out with pattern recognition from the examples but that limits me to the case study.

It’s a really good point - we added a link to the SSMSE user manual in the R help documentation (nmfs-fish-tools/SSMSE@1452b0a).

The additions to the manual for the om_list and sample_struct are quite helpful. The link in the R help isn't working as roxygen doesn't use markdown formatting, I believe the correct format is \href{https://}{text}.

Not required for the paper revision, but I'd also recommend using the term 'projection' as much as possible in the manual when referencing the simulations. "Future changes to the OM" sounds like it refers to an update in the functionality of the software in a later version.

Paper comments:

Line 32: I don't like using the word "realistic" here as all models are simplifications of the real world. Recommend "developing sufficient OMs.." or "developing sufficient OMs for evaluating management strategies is intensive" and leave it at that.

Line 76: "file directories" instead of "names and locations"?

Line 106: Assessment error is also an emergent property of the estimation algorithm, e.g., retrospective bias. The simulation itself, i.e., model fitting in the projection, allows one to replicate these dynamics as part of the management procedure evaluation.

Line 122: Markdown formatting issue.

[k-doering-NOAA]

@editorialbot generate pdf

[editorialbot]

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

[k-doering-NOAA]

thanks @quang-huynh , I added your changes to the paper, which should show up in the newly generated version.

Thanks for the manual suggestions, too, I turned on markdown formatting for Roxygen so that it renders properly.

[k-doering-NOAA]

@iagomosqueira, let me know if there are additional changes I should make to meet your checklist. Thank you!

[iagomosqueira]

Thanks @k-doering-NOAA, I think it is all good to go now.

[k-doering-NOAA]

Good to hear, thank you. @sbenthall , what are the next steps?

[sbenthall]

Amazing! The reviewers have recommended acceptance and we can proceed!! I'm so glad.

The final steps are:

• Generate a PDF and do final proof-reading. I'll run that command next.
• @k-doering-NOAA , after final proof-reading, can you please tag the release on the repository, and reporting that tag to me to be associated with the submission
• Then, you'll need to upload an archive of the release, with the correct metadata, to Zenodo and report the DOI here so I can associate it with the submission.

[sbenthall]

@editorialbot generate pdf

[editorialbot]

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

[k-doering-NOAA]

@sbenthall the tag is v0.2.7 (https://github.com/nmfs-fish-tools/SSMSE/tree/v0.2.7)

We proofread the draft and made small fixes. I noticed Sean Anderson was listed as a reviewer, even though he ultimately did not review - I don't know how to fix this.

I'll work on Zonodo now.

[k-doering-NOAA]

Ok, Zonodo DOI: 10.5281/zenodo.8394821

[sbenthall]

@editorialbot remove @seananderson from reviewers

[editorialbot]

@seananderson removed from the reviewers list!

[sbenthall]

@editorialbot generate pdf

[editorialbot]

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

[sbenthall]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1371/journal.pone.0092725 is OK
- 10.1577/1548-8446(2006)31[590:TCFIE]2.0.CO;2 is OK
- 10.1126/science.1149016 is OK
- 10.1002/fsh.10131 is OK
- 10.1016/j.fishres.2020.105725 is OK
- 10.7755/TMSPO.183 is OK
- 10.1016/j.fishres.2020.105854 is OK
- 10.1139/f03-109 is OK
- 10.1016/j.fishres.2018.12.014 is OK
- 10.1016/j.fishres.2012.10.012 is OK
- 10.2760/18924 is OK
- 10.1016/j.fishres.2022.106229 is OK
- 10.1111/faf.12104 is OK
- 10.1016/j.fishres.2021.106180 is OK
- 10.1006/jmsc.2000.0737 is OK
- 10.1139/cjfas-2020-0257 is OK
- 10.1111/j.1467-2979.2011.00417.x is OK
- 10.1111/faf.12480 is OK
- 10.1016/j.fishres.2021.105924 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[sbenthall]

@editorialbot set 10.5281/zenodo.8394821 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.8394821

[sbenthall]

@editorialbot set v0.2.7 as version

[editorialbot]

Done! version is now v0.2.7

[sbenthall]

This has been a long journey.

@k-doering-NOAA thank you for your patience and for your fantastic contribution.

Thank you @iagomosqueira and @quang-huynh for your reviews.

I recommend this submission for acceptance to JOSS.

[sbenthall]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1371/journal.pone.0092725 is OK
- 10.1577/1548-8446(2006)31[590:TCFIE]2.0.CO;2 is OK
- 10.1126/science.1149016 is OK
- 10.1002/fsh.10131 is OK
- 10.1016/j.fishres.2020.105725 is OK
- 10.7755/TMSPO.183 is OK
- 10.1016/j.fishres.2020.105854 is OK
- 10.1139/f03-109 is OK
- 10.1016/j.fishres.2018.12.014 is OK
- 10.1016/j.fishres.2012.10.012 is OK
- 10.2760/18924 is OK
- 10.1016/j.fishres.2022.106229 is OK
- 10.1111/faf.12104 is OK
- 10.1016/j.fishres.2021.106180 is OK
- 10.1006/jmsc.2000.0737 is OK
- 10.1139/cjfas-2020-0257 is OK
- 10.1111/j.1467-2979.2011.00417.x is OK
- 10.1111/faf.12480 is OK
- 10.1016/j.fishres.2021.105924 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

Element doi: [facet 'pattern'] The value  is not accepted by the pattern '10\.[0-9]{4,9}/.{1,200}'.

[danielskatz]

👋 @openjournals/dev - help please!

[arfon]

@sbenthall – I wonder if it's this line, where the DOI is double-wrapped {{ doi }}. Perhaps update it to be the same as others { doi }

[sbenthall]

@k-doering-NOAA Hello. It looks like a formatting error in your paper.bib file is blocking the robot from accepting you paper! Can you please correct this?

After making that change, please create a new release and archive DOI and tell me, so that everything is synced up. :)

[k-doering-NOAA]

Hi @sbenthall,

the new tag is v0.2.8 and DOI is 10.5281/zenodo.10014307

Hopefully that fixes the issue!

[sbenthall]

@editorialbot set v0.2.8 as version

[editorialbot]

Done! version is now v0.2.8

[sbenthall]

@editorialbot set 10.5281/zenodo.10014307 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10014307

[sbenthall]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1371/journal.pone.0092725 is OK
- 10.1577/1548-8446(2006)31[590:TCFIE]2.0.CO;2 is OK
- 10.1126/science.1149016 is OK
- 10.1002/fsh.10131 is OK
- 10.1016/j.fishres.2020.105725 is OK
- 10.7755/TMSPO.183 is OK
- 10.1016/j.fishres.2020.105854 is OK
- 10.1139/f03-109 is OK
- 10.1016/j.fishres.2018.12.014 is OK
- 10.1016/j.fishres.2012.10.012 is OK
- 10.2760/18924 is OK
- 10.1016/j.fishres.2022.106229 is OK
- 10.1111/faf.12104 is OK
- 10.1016/j.fishres.2021.106180 is OK
- 10.1006/jmsc.2000.0737 is OK
- 10.1139/cjfas-2020-0257 is OK
- 10.1111/j.1467-2979.2011.00417.x is OK
- 10.1111/faf.12480 is OK
- 10.1016/j.fishres.2021.105924 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

:wave: @openjournals/ese-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4701, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[k-doering-NOAA]

@sbenthall , anything needed from the authors on this?

[sbenthall]

@k-doering-NOAA Not that I know of. The next step is that an Editor-in-Chief is supposed to finalize the acceptance. That might be @kthyng

[kthyng]

Yep ok my steps are

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

[kthyng]

@k-doering-NOAA We usually ask that authors change the metadata in the zenodo archive to match the JOSS title and author list — would you mind doing this?

[kthyng]

@k-doering-NOAA Please check the capitalization in your references. You can preserve capitalization by placing {} around characters/words in your .bib file.

[k-doering-NOAA]

@kthyng I just changed the Zenodo metadata title to match the JOSS title. Author list already matches.

For the references, do I need to edit the .bib file and resubmit to Zenodo again?

[kthyng]

Yes edit the .bib and let's regenerate the pdf to check everything. No need to resubmit to Zenodo since it is just the paper text changing.

[k-doering-NOAA]

@kthyng, thank you, I made changes to the bib and pushed them to the main branch (https://github.com/nmfs-fish-tools/SSMSE). I used the JOSS paper draft github action to generate an informal proof and I think the capitalization issue is fixed. Thanks for the tip about {}!

[k-doering-NOAA]

@kthyng let me know if anything else needs to be fixed.