[REVIEW]: fishRman: A Shiny R Dashboard improving Global Fishing Watch data availability

[whedon]

Submitting author: @Shyentist (Pasquale Buonomo)
Repository: https://github.com/Shyentist/fish-r-man
Version: v1.0.0
Editor: @KristinaRiemer
Reviewer: @jules32, @HeatherWelch
Archive: 10.5281/zenodo.5582567

⚠️ JOSS reduced service mode ⚠️

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Status

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Markdown: [![status](https://joss.theoj.org/papers/9895e0e14fbd2be0622022dbbe15fe10/status.svg)](https://joss.theoj.org/papers/9895e0e14fbd2be0622022dbbe15fe10)

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

@jules32 & @HeatherWelch, 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 @KristinaRiemer 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 @jules32

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 (@Shyentist) 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?

Review checklist for @HeatherWelch

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 (@Shyentist) 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. @jules32, @HeatherWelch 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]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (709.7 files/s, 88755.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
JSON                            19             27              0           1923
R                               11            265             63           1758
Markdown                         5             46              0            165
CSS                              1             85              0            147
TeX                              1             16              0            132
-------------------------------------------------------------------------------
SUM:                            37            439             63           4125
-------------------------------------------------------------------------------


Statistical information for the repository '1f71e8d768c9244d0ccab880' was
gathered on 2021/07/09.
No commited files with the specified extensions were found.

[whedon]

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.32614/RJ-2018-009 is OK
- 10.5281/zenodo.4679424 is OK

MISSING DOIs

- 10.21105/joss.00848 may be a valid DOI for title: countrycode: An R package to convert country names and country codes

INVALID DOIs

- None

[whedon]

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

[KristinaRiemer]

Hi @Shyentist, thanks again for your JOSS submission! This is to notify you that I'm going to be on vacation July 14 - August 8. Hopefully you and the submission reviewers @jules32 and @HeatherWelch will be able to make progress on this submission's review in my absence. If anything urgent comes up during that time period, feel free to contact EiC @arfon. If you have any questions right now, please let me know.

[KristinaRiemer]

/ooo July 14 until August 8

[whedon]

👋 @jules32, please update us on how your review is going (this is an automated reminder).

[whedon]

👋 @HeatherWelch, please update us on how your review is going (this is an automated reminder).

[jules32]

Hi! I'll be reviewing by mid-week next week.

[jules32]

@whedon commands

[whedon]

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

[jules32]

👋 @arfon @whedon

I'm logged in but unfortunately it looks like my review invitation has expired. I know Kristina is out, would you be able to help?

https://github.com/openjournals/joss-reviews/invitations

[danielskatz]

@whedon re-invite @jules32 as reviewer

[whedon]

OK, the reviewer has been re-invited.

@jules32 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

[HeatherWelch]

@whedon it seems like my review invitation has also expired [image: Screen Shot 2021-07-26 at 7.25.23 AM.png]

…

On Sun, Jul 25, 2021 at 5:03 PM whedon ***@***.***> wrote: OK, the reviewer has been re-invited. @jules32 <https://github.com/jules32> please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3467 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFTRCYECOFHOZITEKJUISTDTZSQ3TANCNFSM5ADNDNKQ> .

-- *Heather Welch* Project Scientist UCSC and NOAA SWFSC Environmental Research Division 99 Pacific St. Suite 255A Monterey, CA *93940* phone (wk): 831-648-8516 <http://conservationplanning.org/people/heather-welch/> http://conservationplanning.org/people/heather-welch/ https://github.com/HeatherWelch

[whedon]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

[danielskatz]

@whedon re-invite @HeatherWelch as reviewer

[whedon]

OK, the reviewer has been re-invited.

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

[HeatherWelch]

@Shyentist a couple questions/issues:

1. I am not able to get the visualize button to work, either by converting the currently queried csv or by uploading a .gpkg.
2. Would it be possible to clear the forms on the analysis page when starting a new analysis? E.g. in this situation I am not sure if I'm analyzing the current query or the uploaded .gpkg:

[Shyentist]

Hello @HeatherWelch .

1. What do you mean that the button does not work? Does it remain greyed out? Does it do nothing upon clicking? I am unable to replicate the issue.
2. As of now, no, but that would be a nice addition indeed. EDIT: The analyses are always performed on the latest data loaded onto the Analysis tab.

[Shyentist]

@KristinaRiemer I am trying. I added a .zenodo.json to the root directory, but I don't know how to continue from here. This step was suggested by Zenodo under Metadata

EDIT: Found it!

[KristinaRiemer]

You should be able to edit it via Zenodo's user interface, I think?

[Shyentist]

It should be okay now. Sorry, it is my first time uploading to Zenodo, and releasing on GitHub in general.

[KristinaRiemer]

It's all good! Thanks for taking the time to figure that out.

[KristinaRiemer]

@whedon set 10.5281/zenodo.5582567 as archive

[whedon]

OK. 10.5281/zenodo.5582567 is the archive.

[KristinaRiemer]

@whedon set v1.0.0 as version

[whedon]

OK. v1.0.0 is the version.

[KristinaRiemer]

@whedon recommend-accept

[whedon]

Attempting dry run of processing paper acceptance...

[KristinaRiemer]

@Shyentist a JOSS EiC will review this now before publishing!

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2697

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2697, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[Kevin-Mattheus-Moerman]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

🚨🚨🚨 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.03467 joss-papers#2699
1. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03467
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...

[Kevin-Mattheus-Moerman]

Congratulations @Shyentist on getting this work published in JOSS!

Thanks @KristinaRiemer for editing this, and thank you @jules32 and @HeatherWelch for your review efforts!!!

[whedon]

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

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

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[Shyentist]

Thank you, everyone @Kevin-Mattheus-Moerman @KristinaRiemer @jules32 @HeatherWelch for all your efforts and suggestions that helped make fishRman better 🙇🏻

[jules32]

Congratulations!!!

…

On Thu, Oct 21, 2021 at 8:47 AM Pasquale Buonomo ***@***.***> wrote: Thank you, everyone @Kevin-Mattheus-Moerman <https://github.com/Kevin-Mattheus-Moerman> @KristinaRiemer <https://github.com/KristinaRiemer> @jules32 <https://github.com/jules32> @HeatherWelch <https://github.com/HeatherWelch> for all your efforts and suggestions that helped make fishRman better 🙇🏻 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3467 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABM6ORPONY47NBH4NIRN7KTUIAYXPANCNFSM5ADNDNKQ> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Julia Stewart Lowndes, PhD Openscapes Co-Director National Center for Ecological Analysis and Synthesis (NCEAS <https://www.nceas.ucsb.edu/>) University of California, Santa Barbara (UCSB) Openscapes <https://openscapes.org> • Ocean Health Index <http://ohi-science.org/> • Mozilla Fellow website <http://jules32.github.io/> • github <https://github.com/jules32> • twitter <https://twitter.com/juliesquid>