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[PRE REVIEW]: SSMSE: An R package for Management Strategy Evaluation with Stock Synthesis Operating Models
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: Pending Managing EiC: Kevin M. Moerman
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HTML: <a href="https://joss.theoj.org/papers/9af77892379058580aced7199f3dc6dd"><img src="https://joss.theoj.org/papers/9af77892379058580aced7199f3dc6dd/status.svg"></a>
Markdown: [](https://joss.theoj.org/papers/9af77892379058580aced7199f3dc6dd)
Author instructions
Thanks for submitting your paper to JOSS @k-doering-NOAA. Currently, there isn't a JOSS editor assigned to your paper.
@k-doering-NOAA if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).
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
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:
@editorialbot generate pdf
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
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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
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SUM: 104 1507 3002 18935
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gitinspector failed to run statistical information for the repository
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
@k-doering-NOAA thanks for this submission. I am a JOSS AEiC and here to help process initial steps.
-
[x] Can you check those potentially missing/invalid DOIs? :point_up: You can check the references gain by calling
@editorialbot check references. -
[x] 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.
@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.
@KristinaRiemer do you think you could edit this one once you are available?
👋 @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.
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!
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
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
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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?
@Kevin-Mattheus-Moerman my current submissions are going a bit slowly, but I can definitely edit this submission once one of those are done!
@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)
Maybe you could try encoding the offending part... doing that gives 10.1577/1548-8446%282006%2931%5B590%3ATCFIE%5D2.0.CO%3B2
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
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
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
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
@lorenzo-rovigatti thanks for the suggestion! I gave it a try, (with a few variations of using escapes and grouping using curly braces) but the editorial bot is still marking the DOI as invalid