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

editorialbot commented 2 years ago

Submitting author: !--author-handle-->@VLucet@Bisaloo<!--end-editor-- Reviewers: @quang-huynh, @kellijohnson-NOAA Archive: 10.5281/zenodo.8015102

Status

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

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

@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

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @Bisaloo 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 @quang-huynh

📝 Checklist for @kellijohnson-NOAA

Bisaloo commented 1 year ago

It is possible to edit the metadata on zenodo, which is what we usually do to reflect the authors on the paper. If you are not able to do it, it's not a big deal, we can wave this requirement, which is why I didn't mention it in my last message.

VLucet commented 1 year ago

@Bisaloo I believe I was able to update the metadata.

Bisaloo commented 1 year ago

@editorialbot set 10.5281/zenodo.8015102 as archive

editorialbot commented 1 year ago

Done! archive is now 10.5281/zenodo.8015102

Bisaloo commented 1 year ago

@editorialbot set v1.0.0 as version

editorialbot commented 1 year ago

Done! version is now v1.0.0

VLucet commented 1 year ago

Thanks for the PR @Bisaloo, I merged it.

Bisaloo commented 1 year ago

@editorialbot generate pdf

Bisaloo commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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 commented 1 year ago

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

Bisaloo commented 1 year ago

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

VLucet commented 1 year ago

just saw, I merged it

Bisaloo commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

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

Bisaloo commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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 commented 1 year ago

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

ID ref-thorson_importance_2015 already defined

VLucet commented 1 year ago

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

VLucet commented 1 year ago

It should be fixed now.

Bisaloo commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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 commented 1 year ago

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

VLucet commented 1 year ago

Looks good to me.

kthyng commented 1 year ago

Here is my to do list:

[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 commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

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 commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/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 commented 1 year ago

Congratulations @VLucet @eric-pedersen :tada::tada:!

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

VLucet commented 1 year ago

Yay! Thanks to you @Bisaloo as well!

kthyng commented 1 year ago

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 commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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  <img src="https://joss.theoj.org/papers/10.21105/joss.04724/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04724/status.svg
   :target: https://doi.org/10.21105/joss.04724

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