[REVIEW]: mmrefpoints: Projecting long-term marine mammal abundance with bycatch

[whedon]

Submitting author: @mcsiple (Margaret Siple)
Repository: https://github.com/mcsiple/mmrefpoints
Branch with paper.md (empty if default branch):
Version: v 1.0.1
Editor: @fboehm
Reviewers: @ha0ye, @tbrown122387
Archive: 10.5281/zenodo.6338110

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Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/548532c08c82cf64015d5440c495a466/status.svg)](https://joss.theoj.org/papers/548532c08c82cf64015d5440c495a466)

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

@ha0ye, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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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 ✨

Review checklist for @ha0ye

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@mcsiple) 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

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 and who the target audience is?
• 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?

@tbrown122387, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

1. Make sure you're logged in to your GitHub account
2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fboehm 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 ✨

Review checklist for @tbrown122387

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
• 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 (@mcsiple) 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

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 and who the target audience is?
• 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?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ha0ye and @eirenjacobson it looks like you're currently assigned to review this paper 🎉.

⚠️ JOSS reduced service mode ⚠️

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

2. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1309

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.10 s (745.6 files/s, 130135.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                             7            208             92           3429
R                               46            487           1472           3388
JSON                             2              7              0            681
Rmd                              8            445            993            606
Markdown                         5            108              0            398
TeX                              2             27              0            366
YAML                             3              2              4             29
-------------------------------------------------------------------------------
SUM:                            73           1284           2561           8897
-------------------------------------------------------------------------------


Statistical information for the repository 'fc9602a544d20e3515f37bef' was
gathered on 2021/11/04.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.1111/j.1748-7692.1998.tb00688.x is OK
- 10.1111/mms.12427 is OK
- 10.1644/11-MAMM-A-291.1 is OK
- 10.1093/icesjms/fsy049 is OK
- 10.1139/f84-058 is OK
- 10.2989/025776195784156511 is OK
- 10.1890/14-1990 is OK
- 10.1002/ece3.4772 is OK
- 10.7557/3.2747 is OK
- 10.3389/fmars.2021.735770 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

PDF failed to compile for issue #3888 with the following error:

 [WARNING] Citeproc: citation eirenjacobson not found
Error producing PDF.
! Undefined control sequence.
\hyper@@link ->\let \Hy@reserved@a 
                                   \relax \@ifnextchar [{\hyper@link@ }{\hyp...
l.386 }

Looks like we failed to compile the PDF

[fboehm]

@whedon re-invite @eirenjacobson as reviewer

[whedon]

OK, the reviewer has been re-invited.

@ @eirenjacobson please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[fboehm]

@whedon re-invite @ha0ye as reviewer

[whedon]

@ha0ye already has access.

[fboehm]

@whedon generate pdf

[whedon]

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

[fboehm]

@ha0ye and @eirenjacobson - how are the reviews coming along? Please let me know if you have any questions. Thanks again!!

[fboehm]

@eirenjacobson - Did you have a chance to accept the invitation? (in the thread above)
If the link has expired, please let me know. Thanks again!

[ha0ye]

I haven't started yet, but it's on my calendar.

[eirenjacobson]

@fboehm when I click that link I get the message "Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account."

[fboehm]

Hi, @eirenjacobson - sorry for my error. Can you check to see if you can check the boxes in the checklist? Just try to check one, to see if the checkmark appears, then uncheck it, assuming that you haven't actually verified that piece of information for the review. I think that there was an issue with your invitation, but the bot whedon may have resolved it. Thanks again!

[eirenjacobson]

No, I can't check the boxes :(

[fboehm]

Thanks for checking. I'll re-invite you now via the bot.

[fboehm]

@whedon re-invite @eirenjacobson as reviewer

[whedon]

OK, the reviewer has been re-invited.

@eirenjacobson please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[eirenjacobson]

I'm all set now, thanks!

[eirenjacobson]

Hi all, I had planned to complete this review this week but I am currently participating in strike action to improve UK higher education staff pension, pay, equality and working conditions (for more information, see https://www.ucu.org.uk/article/11896/Why-were-taking-action). I will try to complete my review when I return from strike next week.

[mcsiple]

Thank you for letting us know @eirenjacobson and power to the people!

[kyleniemeyer]

@editorialbot generate pdf

[editorialbot]

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

[kyleniemeyer]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03888 joss-papers#3040
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03888
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[mcsiple]

Upon step 0, I found that one of the authors has an extra L in his name in paper.md🤦🏻‍♀️ It's correct everywhere else and I just fixed it. What do I do next? Sorry for the inconvenience...

[kyleniemeyer]

@arfon can you correct the published paper?

[mcsiple]

Found two more copy edits in paper.md (sorry, and thank you)-- see below.

[arfon]

@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

- 10.1111/j.1748-7692.1998.tb00688.x is OK
- 10.1111/mms.12427 is OK
- 10.1644/11-MAMM-A-291.1 is OK
- 10.1093/icesjms/fsy049 is OK
- 10.1139/f84-058 is OK
- 10.2989/025776195784156511 is OK
- 10.1890/14-1990 is OK
- 10.1002/ece3.4772 is OK
- 10.7557/3.2747 is OK
- 10.3389/fmars.2021.757330 is OK
- 10.3389/fmars.2021.752356 is OK
- 10.3389/fmars.2021.735770 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

⚠️ Error preparing acceptance.

[arfon]

@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

- 10.1111/j.1748-7692.1998.tb00688.x is OK
- 10.1111/mms.12427 is OK
- 10.1644/11-MAMM-A-291.1 is OK
- 10.1093/icesjms/fsy049 is OK
- 10.1139/f84-058 is OK
- 10.2989/025776195784156511 is OK
- 10.1890/14-1990 is OK
- 10.1002/ece3.4772 is OK
- 10.7557/3.2747 is OK
- 10.3389/fmars.2021.757330 is OK
- 10.3389/fmars.2021.752356 is OK
- 10.3389/fmars.2021.735770 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof 👉 openjournals/joss-papers#3052

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#3052, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[arfon]

@editorialbot accept

[editorialbot]

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

[editorialbot]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[editorialbot]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03888 joss-papers#3053
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03888
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[arfon]

@kyleniemeyer – this should be updated now. Note that the new PDF might take a few hours to show up on the JOSS site due to caching.

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03888/status.svg)](https://doi.org/10.21105/joss.03888)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03888">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03888/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03888/status.svg
   :target: https://doi.org/10.21105/joss.03888

This is how it will look in your documentation:

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