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[REVIEW]: fishRman: A Shiny R Dashboard improving Global Fishing Watch data availability #3467

Closed whedon closed 2 years ago

whedon commented 3 years ago

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

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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

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @HeatherWelch

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

KristinaRiemer commented 2 years ago

So for the paper, I totally overlooked that the "Summary" section is missing some content. You do a great job of describing the gap, which is that high computational skill level is currently needed to use the Global Fishing Watch data. But there's no mention of your software or how it fills that gap in that section. I think all that is needed is another paragraph at the end that states something along the lines of "The Shiny dashboard fishRman fills this need by..."

Otherwise, there were only a few minor typos in the text:

For the references, some of the capitalization of titles didn't render how it is in the bibtex file. Apparently this can be fixed by putting extra curly brackets around the titles. For example, title = {countrycode: An R package to convert country names and country codes}, should be title = {{countrycode: An R package to convert country names and country codes}},, I think. It looks like there are a handful of reference titles that could be fixed with this approach.

The whedon DOI checker in the above comment shows that three of the references have missing DOIs. Those DOIs are actually fine, but apparently the best practice when there is a DOI number is to put it by itself into the doi field as opposed to putting the entire doi.org url into the url field, so this is probably the approach that should be taken for all of the doi numbers. It's also fine to have both doi and url fields, if there's a URL in addition to the DOI that can be included in a reference.

I'm still working on checking reference links and authors and such, but if you could take care of these tasks for now, that would be helpful!

Shyentist commented 2 years ago

@KristinaRiemer Thank you for proofreading, I got more or less the same results. Line 26 is okay, the word is "public" as in "a group of people having common interests or characteristics. Specifically: the group at which a particular activity or enterprise aims". Line 57 I trust your judgement, because I googled "how to credit financial support" and found that sentence.

I noticed the thing about the doi field, and it has been fixed with the latest commits, while I completely missed the capitalization issue. On it.

EDIT: The capitalization issue remains, even with double curly brackets. I'll look for another solution.

EDIT 2: The solution would be the right one bibtex-wise, because https://bibtex.online/ gives me the reference we are aiming for when using double curly brackets on the entire title. Maybe the compiler bot does something more (or less, since it seems to ignore this particular use of nested curly brackets, but not others)?

EDIT 3: I have tried many variations for curly brackets, in number and position, but nothing seems to solve this.

Shyentist commented 2 years ago

Apparently, the curly brackets within curly brackets keep the elements as they are, so I also have to edit the author fields for Tyler Clavelle and Mayorga. They are cited in text by full name and, in the references, are in alphabetical order by name rather than surname.

EDIT: Wrapping their names in single, rather than double, curly brackets does not solve the issue.

EDIT 2: It seems to be related to the fact that the work cited is a webpage, leading to the names being quoted like that (the correct way according to bibtex).

Shyentist commented 2 years ago

So for the paper, I totally overlooked that the "Summary" section is missing some content. You do a great job of describing the gap, which is that high computational skill level is currently needed to use the Global Fishing Watch data. But there's no mention of your software or how it fills that gap in that section. I think all that is needed is another paragraph at the end that states something along the lines of "The Shiny dashboard fishRman fills this need by..."

Isn't this covered by the Statement of need?

Shyentist commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

Shyentist commented 2 years ago

@whedon check references

whedon commented 2 years ago 
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
- 10.21105/joss.00848 is OK
- 10.1002/ecs2.2753 is OK
- 10.1002/bmb.21230 is OK
- 10.1002/ecs2.2567 is OK

MISSING DOIs

- None

INVALID DOIs

- None
Shyentist commented 2 years ago

@KristinaRiemer hi again!

I think I managed to solve the capitalization issue. I amended the lines you mentioned, and solved the full name issue for the websites (how this one got solved is a mystery to me, but now it works properly).

With the current pdf, I see only one issue, which is "tidiverse" not capitalized (it is not capitalized when retrieving the bib reference from the package, but the paper's title is capitalized)

Also, statement of need question still pending.

KristinaRiemer commented 2 years ago

Ah, I didn't know about that way of using the word "public", that's great!

Now that I re-reading the "What should my paper contain?" guidelines, I think what you have for the summary section is sufficient. I was overinterpreting the summary section definition.

Thank you for making all of those fixes to the capitalization of titles and the DOI links! This formatting stuff can be very fiddly.

You should be able to hand edit the .bib file where there are errors? So for the tidyverse title missing the capitalization, shouldn't you be able to change it to a capital T?

It looks like there are a couple other references that also have weird formatting due to their bib references from citation. The viridis package entry and the maps package entry both have weird author lists, which I think will need to be hand edited to the correct format of {firstname lastname and firstname lastname}, e.g., {Simon Garnier and Noam Ross and...}.

The ggplot2 reference on line 105 is incomplete, I think due to a missing start curly bracket in the author field for that reference?

The only other minor error I'm seeing is that the link to the stringi reference appears to be broken, or at least returns a 404 error for me. The correct URL might be https://stringi.gagolewski.com/?

Shyentist commented 2 years ago

You should be able to hand edit the .bib file where there are errors? So for the tidyverse title missing the capitalization, shouldn't you be able to change it to a capital T?

Yes, I meant to ask which of the two was the correct one in your opinion. I'll go with capital T

It looks like there are a couple other references that also have weird formatting due to their bib references from citation. The viridis package entry and the maps package entry both have weird author lists, which I think will need to be hand edited to the correct format of {firstname lastname and firstname lastname}, e.g., {Simon Garnier and Noam Ross and...}.

I noticed that too. I left them as I found them via R's citation function, waiting for instructions. I will edit them to fit the general style.

The ggplot2 reference on line 105 is incomplete, I think due to a missing start curly bracket in the author field for that reference?

Yes, on it.

The only other minor error I'm seeing is that the link to the stringi reference appears to be broken, or at least returns a 404 error for me. The correct URL might be https://stringi.gagolewski.com/?

You are most likely correct. Once again, I trusted R's citation function too much.

Shyentist commented 2 years ago

@whedon generate pdf

whedon commented 2 years ago

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

Shyentist commented 2 years ago

@KristinaRiemer I have made amendments in accordance with the feedback. It gets easier once one knows how TeX works.

Shyentist commented 2 years ago

@jules32 I have read through the Divio material you advised. It makes a lot of sense, and I'll be more aware of these principles when rewriting the documentation. Thank you very much 😄

KristinaRiemer commented 2 years ago

Thanks for making all of those changes @Shyentist! I'm actually surprised that so many of the citations from citations had errors and such, I would think we should be able to trust that they'll be correct.

I think the paper looks good now. The next steps are to: 1) create a tagged release of the repo on GitHub and 2) archive the code (in Zenodo, figshare, institutional repository, etc.) to generate a DOI. If you can post a link to the DOI here when you're done please.

Shyentist commented 2 years ago

Great! @KristinaRiemer I have a practical question before I create a release. I would like to have the footer of the app to show, under References, the paper, and possibly link to it, but the article is only published after the release. Will I need to change the footer immediately after the release, or is there a way for me to insert an anchor (maybe the DOI in the draft by whedon?) that is not operational now (404 page not found when clicked), but will be operational after the publishing?

KristinaRiemer commented 2 years ago

@Shyentist the DOI in the generated PDF will be the one for the published paper. It's actually generated from the review issue #, which is 3467 for your submission. I wasn't actually sure about how DOIs were created, I had to ask someone else, so thanks for bringing this up! Feel free to add that DOI to the app and then do the release and archive.

Shyentist commented 2 years ago

@KristinaRiemer thank you for asking about the DOI. I figured it was generated that way, but better not to assume 😄 About the citations from R's function, I asked around, and they might be "wrong" in our context, but right for the publication or database they were aiming for.

I created the release and this is the Zenodo DOI: 10.5281/zenodo.5582568 (full URL https://doi.org/10.5281/zenodo.5582567)

KristinaRiemer commented 2 years ago

That's good to know about the different applications of the citations function!

Could you edit the Zenodo archive title to match the title of the paper? We like to have the archive and paper have the same title and author list for consistency.

Shyentist commented 2 years ago

@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 image

EDIT: Found it!

KristinaRiemer commented 2 years ago

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

Screen Shot 2021-10-20 at 12 00 16 PM
Shyentist commented 2 years ago

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

KristinaRiemer commented 2 years ago

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

KristinaRiemer commented 2 years ago

@whedon set 10.5281/zenodo.5582567 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5582567 is the archive.

KristinaRiemer commented 2 years ago

@whedon set v1.0.0 as version

whedon commented 2 years ago

OK. v1.0.0 is the version.

KristinaRiemer commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago 
Attempting dry run of processing paper acceptance...
KristinaRiemer commented 2 years ago

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

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2697

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/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 commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago 
Doing it live! Attempting automated processing of paper acceptance...
whedon commented 2 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 2 years ago

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

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2699
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03467
  3. If everything looks good, then close this review issue.

  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

    Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 2 years ago

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 commented 2 years ago

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

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Shyentist commented 2 years ago

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

jules32 commented 2 years ago

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 https://github.com/openjournals/joss-reviews/issues/3467#issuecomment-948738921, 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.

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