[PRE REVIEW]: SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models #4536

editorialbot · 2022-07-01T21:21:15Z

Submitting author: @k-doering-NOAA (Kathryn Doering)
Repository: https://github.com/nmfs-fish-tools/ssmse
Branch with paper.md (empty if default branch):
Version: v0.2.6
Editor: @sbenthall
Reviewers: @seananderson, @quang-huynh
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/9af77892379058580aced7199f3dc6dd/status.svg)](https://joss.theoj.org/papers/9af77892379058580aced7199f3dc6dd)

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

editorialbot · 2022-07-01T21:21:17Z

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:

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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 · 2022-07-01T21:21:20Z

Software report:

github.com/AlDanial/cloc v 1.88  T=0.11 s (917.0 files/s, 206719.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               58            566           2362           8736
Scheme                          19             18              0           7830
Markdown                         5            176              0            994
Rmd                              8            336            612            539
CSS                              1             66              1            275
TeX                              1            270              0            274
YAML                            11             17             19            204
HTML                             1             58              8             83
-------------------------------------------------------------------------------
SUM:                           104           1507           3002          18935
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

editorialbot · 2022-07-01T21:21:21Z

Wordcount for paper.md is 3415

editorialbot · 2022-07-01T21:21:28Z

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

OK DOIs

- 10.1371/journal.pone.0092725 is OK
- 10.1126/science.1149016 is OK
- 10.7755/TMSPO.183 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
- 10.1111/faf.12104 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
- 10.1016/j.fishres.2021.105924 is OK

MISSING DOIs

- 10.1002/fsh.10131 may be a valid DOI for title: Handle with care: establishing catch limits for fish stocks experiencing episodic natural mortality events
- 10.1016/j.fishres.2020.105725 may be a valid DOI for title: An integrated tagging and catch-curve model reveals high and seasonally-varying natural mortality for a fish population at low stock biomass
- 10.1016/j.fishres.2020.105854 may be a valid DOI for title: Spatial population dynamics of eastern oyster in the Chesapeake Bay, Maryland
- 10.1016/j.fishres.2022.106229 may be a valid DOI for title: Playing the detective: Using multispecies approaches to estimate natural mortality rates
- 10.1016/j.fishres.2021.106180 may be a valid DOI for title: Indexing starvation mortality to assess its role in the population regulation of Northern cod
- 10.1111/faf.12480 may be a valid DOI for title: Operating model design in tuna Regional Fishery Management Organizations: Current practice, issues and implications

INVALID DOIs

- 10.1577/1548-8446(2006)31\[590:TCFIE\]2.0.CO;2 URL is INVALID

editorialbot · 2022-07-01T21:21:49Z

⚠️ An error happened when generating the pdf.

Kevin-Mattheus-Moerman · 2022-07-01T21:50:21Z

@k-doering-NOAA thanks for this submission. I am a JOSS AEiC and here to help process initial steps.

Can you check those potentially missing/invalid DOIs? ☝️ You can check the references gain by calling @editorialbot check references.
There is a paper compilation error:

Problem with ORCID (00000-0002-0396-7044) for Kathryn Doering. ORCID looks to be the wrong length (Theoj::Error)

Looks like it should have 4 zeros at the start, not 5: https://orcid.org/0000-0002-0396-7044
Can you fix this and try to compile the paper again? You can call @editorialbot generate pdf here.

Kevin-Mattheus-Moerman · 2022-07-01T21:57:45Z

@k-doering-NOAA I have just added the waitlisted label here because all our editors in this domain are currently handling many other submissions. We will assign a handling editor as soon as one becomes available.

Kevin-Mattheus-Moerman · 2022-07-01T21:58:13Z

@KristinaRiemer do you think you could edit this one once you are available?

danielskatz · 2022-07-05T19:50:06Z

👋 @k-doering-NOAA - note that your paper does not compile. As @Kevin-Mattheus-Moerman says, you at least need to remove the extra 0 in an ORCID. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

k-doering-NOAA · 2022-07-06T13:39:47Z

Thank you @danielskatz and others - I will make changes to the ORCID, check the DOIs, and figure out why the paper isn't compiling within the next few days!

k-doering-NOAA · 2022-07-06T14:54:16Z

@editorialbot check references

editorialbot · 2022-07-06T14:54:31Z

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

OK DOIs

- 10.1371/journal.pone.0092725 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

- 10.1577/1548-8446(2006)31\[590:TCFIE\]2.0.CO;2 URL is INVALID

k-doering-NOAA · 2022-07-06T14:56:28Z

@editorialbot check references

editorialbot · 2022-07-06T14:56:46Z

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

OK DOIs

- 10.1371/journal.pone.0092725 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

- 10.1577/1548-8446(2006)31[590:TCFIE]2.0.CO;2 URL is INVALID

k-doering-NOAA · 2022-07-06T14:58:47Z

@editorialbot generate pdf

editorialbot · 2022-07-06T15:00:00Z

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

k-doering-NOAA · 2022-07-06T15:04:48Z

@Kevin-Mattheus-Moerman and @danielskatz, I fixed most of the DOIs and the paper now compiles with removing 1 0 from the ORCID.

I still am not able to resolve the invalid DOI, I think it has something to do with the [] in the DOI - I thought these characters needed to be esacaped (e.g., \[), but that didn't work, nor did not escaping them ([). The following link works: https://doi.org/10.1577/1548-8446(2006)31[590:TCFIE]2.0.CO;2 . Any suggestions on how I should change the DOI in the .bib file?

k-doering-NOAA · 2022-07-06T15:47:05Z

Potential reviewers: Ecosantos hvoltbb EDiLD

KristinaRiemer · 2022-07-06T19:11:45Z

@Kevin-Mattheus-Moerman my current submissions are going a bit slowly, but I can definitely edit this submission once one of those are done!

k-doering-NOAA · 2022-07-18T12:57:00Z

@danielskatz and @Kevin-Mattheus-Moerman, just wondering if either of you had a suggestion of what to do about the one DOI I cannot figure out how to make valid? (see previous post in thread)

lorenzo-rovigatti · 2022-07-28T12:31:42Z

Maybe you could try encoding the offending part... doing that gives 10.1577/1548-8446%282006%2931%5B590%3ATCFIE%5D2.0.CO%3B2

k-doering-NOAA · 2022-07-28T13:27:03Z

@editorialbot check references

editorialbot · 2022-07-28T13:27:39Z

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

OK DOIs

- 10.1371/journal.pone.0092725 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

- 10.1577/1548-844628200629315B5903ATCFIE5D2.0.CO3B2 is INVALID

k-doering-NOAA · 2022-07-28T13:38:48Z

@editorialbot check references

editorialbot · 2022-07-28T13:38:59Z

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

OK DOIs

- 10.1371/journal.pone.0092725 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

- 10.1577/1548-844628200629315B5903ATCFIE5D2.0.CO3B2 is INVALID

k-doering-NOAA · 2022-07-28T13:51:04Z

@editorialbot check references

editorialbot · 2022-08-12T15:32:04Z

Assigned! @sbenthall is now the editor

sbenthall · 2022-08-12T15:35:18Z

@Ecosantos Would you be able to review this submission?

Ecosantos · 2022-08-16T00:33:39Z

@sbenthall, Thanks for the invitation but, I am not really sure if I can review this submission. Fishery stock assessment has some particular nuances out of my expertise.

I am happy to review anything related to population assessment of non-fishery stocks in the future.

sbenthall · 2022-08-18T19:29:12Z

@HVoltBb Would you be able to review this submission to JOSS?

sbenthall · 2022-08-18T19:29:30Z

@Edild Would you please be able to review this submission to JOSS?

eduardszoecs · 2022-08-30T14:59:16Z

I am on vacation the next 3 weeks and cannot make it.

sbenthall · 2022-08-31T14:19:00Z

@tkchafin Would you be able to review this submission?

sbenthall · 2022-08-31T14:20:31Z

@jsta would you be able to review this submission?

tkchafin · 2022-09-01T08:35:37Z

Sorry, I can't review this one.

jsta · 2022-09-05T12:46:15Z

I can't review either.

sbenthall · 2022-09-19T13:22:49Z

@r-barnes Would you please be able to review this submission?

sbenthall · 2022-09-19T13:23:37Z

@molgor Would you please be able to review this submission?

sbenthall · 2022-09-30T19:48:32Z

@tretherington Would you be able to review this submission?

sbenthall · 2022-09-30T19:49:20Z

@pboesu Would you be able to review this submission?

pboesu · 2022-10-01T18:26:34Z

@sbenthall Unfortunately I am tied up with editorial duties elsewhere. Sorry!

tretherington · 2022-10-02T20:00:21Z

@sbenthall sorry, I'm too busy right now to commit ☹️

sbenthall · 2022-10-20T15:02:37Z

@editorialbot generate pdf

editorialbot · 2022-10-20T15:04:05Z

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

editorialbot · 2022-11-15T14:40:50Z

I can't add that reviewer: seananderson is not a username

sbenthall · 2022-11-15T14:41:08Z

@editorialbot add @seananderson as reviewer

editorialbot · 2022-11-15T14:41:11Z

@seananderson added to the reviewers list!

sbenthall · 2022-11-15T14:41:42Z

Thanks @seananderson for agreeing to be a reviewer!

k-doering-NOAA · 2022-11-15T15:18:43Z

Thank you @seananderson!

sbenthall · 2022-11-15T20:11:57Z

@editorialbot add @quang-huynh as reviewer

editorialbot · 2022-11-15T20:11:59Z

@quang-huynh added to the reviewers list!

sbenthall · 2022-11-15T20:12:28Z

Thank you @quang-huynh for agreeing to be a reviewer!

We have enough reviewers so now we can begin the review process.

sbenthall · 2022-11-15T20:13:42Z

@editorialbot start review

editorialbot · 2022-11-15T20:13:45Z

OK, I've started the review over in #4937.

editorialbot added the pre-review label Jul 1, 2022

editorialbot added R TeX labels Jul 1, 2022

Kevin-Mattheus-Moerman added the waitlisted Submissions in the JOSS backlog due to reduced service mode. label Jul 1, 2022

editorialbot assigned sbenthall Aug 12, 2022

editorialbot closed this as completed Nov 15, 2022

[PRE REVIEW]: SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models #4536

[PRE REVIEW]: SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models #4536

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