Closed whedon closed 2 years ago
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 :tada:.
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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
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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
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SUM: 37 439 63 4125
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Statistical information for the repository '1f71e8d768c9244d0ccab880' was
gathered on 2021/07/09.
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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
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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.
/ooo July 14 until August 8
:wave: @jules32, please update us on how your review is going (this is an automated reminder).
:wave: @HeatherWelch, please update us on how your review is going (this is an automated reminder).
Hi! I'll be reviewing by mid-week next week.
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👋 @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?
@whedon re-invite @jules32 as reviewer
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@jules32 please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
@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 https://github.com/openjournals/joss-reviews/issues/3467#issuecomment-886279815, or unsubscribe https://github.com/notifications/unsubscribe-auth/AFTRCYECOFHOZITEKJUISTDTZSQ3TANCNFSM5ADNDNKQ .
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Heather Welch Project Scientist
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phone (wk): 831-648-8516 http://conservationplanning.org/people/heather-welch/ http://conservationplanning.org/people/heather-welch/ https://github.com/HeatherWelch
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@whedon re-invite @HeatherWelch as reviewer
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@heatherwelch please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
@Shyentist a couple questions/issues:
Hello @HeatherWelch .
Hello @Shyentist,
I’ve completed my first review, thank you for submitting. Below are some comments that I think would benefit your project; they are largely about documentation in various forms.
The Shiny App launched very quickly and was very responsive, and this seems like it will be helpful for researchers wanting to query and analyze Global Fishing Watch data. I think it would benefit from more documentation in the App itself; maybe a landing page that introduces Global Fishing watch with links, describes how people might query and use their data, and describes the data with clear metadata that the user will encounter. Here it would also be appropriate to link the fisheRman Handbook PDF that describes the App’s usage.
Then, on the Query and Analysis tabs, small examples of how to use the App would be very helpful. This could be pre-loaded so that the user can see the example and then clear it to begin their own query. (My first attempts resulted in either “Your query would return more than 1000000 rows” or “Showing 0 to 0 of 0 entries” as I was trying to familiarize myself with the functionality.)
The code itself (global.R, server.R, ui.R) could benefit from more documentation so that it is more clear how all the code works together and so that it could be easier for contributors to navigate and provide any suggestions.
In the paper, I think the statement of need and the state of the field could be more detailed; are there citations and descriptions for who is using the data, how they are using it, what issues they are encountering, and how fisheRman helps? Who is the desired user, what do they have to know, how will this integrate into their workflow?
The fisheRman handbook is very useful; I think it would benefit the user if it were linked from the repo’s README, from the App’s landing page, and from the paper.
Hello @jules32 , thank you for your feedback and advice.
How do we proceed now? Do I make the adjustment and the review goes on from there when I do, or is there anything else with the bot?
Hi @Shyentist,
I have completed my review. Nice work on making GFW data more accessible and easy to manipulate. Below are a few questions and suggestions for improvement.
Query tab.
-Returned table should have column names that match the filter terms, e.g. "hours" in the table should match "vessel_hours" in the filter terms, "cell_II_lat" should match "Latitude", etc.
-For the Flag filter, please link to an ISO look up table and note that these are Alpha 3 Codes. This will be helpful for being who don't know the code of their country of interest.
-For fishing effort at 10th degree there is an option to filter by MMSI; for fishing effort at 100th degree there is an option to filter by MMSI present. It is not clear to me why or how these are different. In the handbook, it would be helpful to have more information on the difference between MMSI and MMSI present filters, and why different options are provided depending on resolution.
Analysis tab.
-It would be helpful if the date range was included somewhere in the map. When writing out a png, it's helpful to maintain information on what time-series e.g. total fishing activity is calculated.
-I am still having trouble with the spatial visualization. It occurs when I convert the current data. Sometimes it doesn't happen, sometimes it does. I just had the error occur with this order of operations:
How do we proceed now? Do I make the adjustment and the review goes on from there when I do, or is there anything else with the bot?
@Shyentist – please make your updates and let us know here when you are ready for the reviewers to take another look. You can update your paper preview at any time with @whedon generate pdf
@arfon Great, thank you!
@HeatherWelch Hi again, thank you for your review and the useful feedback. I am assuming the first list concerns the Handbook, not the paper, apart from the last point.
Query tab
Analysis tab
Visualize
button and results are completely unrelated to the Summarize
button and table. Visualize
creates a latitude-longitude plot, so a map, with the spatial data provided, and is not meant to be a "plotter" for what is summarized. Summarize
, on the other hand, is an aggregator meant to create a new table that can be downloaded as a csv for whatever need the user might have. Basically, Visualize
does not operate on the summarized dataframe, which does not always retain lat-lon information and can reach up to 7 different dimensions, but on the original spatial data.Thanks for providing reviews during my absence, @jules32 and @HeatherWelch! Just to confirm what @arfon said, @Shyentist you should make changes as suggested by the reviewers and feel free to update us when complete or discuss these more here!
@Shyentist just checking in to see how your updates are going...let me know if you need anything!
@KristinaRiemer hi, I have made some improvements for what was pointed out during the first review, and I am working on the actual paper as of now. I will surely let you know in case I need anything, thank you!
@KristinaRiemer hi, I have a question about the paper. One of the points in jules' review was
The fisheRman handbook is very useful; I think it would benefit the user if it were linked from the repo’s README, from the App’s landing page, and from the paper.
I was wondering, if the url for the Handbook changes after the paper, wouldn't that be an issue? What are the rules for updating the paper, if that is even possible?
Are you expecting the handbook URL to change? I think probably as long as that URL is maintained in the GitHub repository README, users will be able to find it.
I think so. If the documentation expands beyond the Handbook, I would like to arrange it in folders as the project goes on. I think the best course of action would be to link to the repository itself, with the README always bearing the updated URL for the Handbook (and whatever else might be needed).
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@KristinaRiemer I think the repository is ready for a second review. Is there something for me to do?
Thanks @Shyentist! The next step would be for @jules32 and @HeatherWelch to review the changes you've made, update the review checklists accordingly, and identify if there is anything remaining that could be addressed.
Hi @shyentist and @KristinaRiemer, I'll be able to do a second review by next Monday; sorry for the delay here but I haven't forgotten!
Hi @jules32, thanks so much for checking in and providing a deadline!
Hi @Shyentist , I’ve re-reviewed and think that you have met most of the checklist required for the JOSS review at this point. You've addressed my previous comments and I think that the Handbook has improved a lot; the Example on p. 12 was especially helpful for understanding how the App could be used. The only thing that I didn’t see in the Software Paper was the “State of the Field”; perhaps https://globalfishingwatch.org/data/working-with-our-downloadable-public-data-in-r/ would be a potential citation for this section.
In the long term (beyond the scope of this JOSS review), I do think that more documentation focused on your primary audience would increase the number of users who use the App, and improve their experience with it. For example, I think the App itself would benefit greatly from some sort of text/banner on the home page that says something like “This is the fishRman app to help you explore and analyze Global Fishing Watch Data. Learn more about Global Fishing Watch and the data available for querying with these links”. I say this because I expect that the App will be the “first contact” for many fisheries researchers, who learn about it from their colleagues who have shared the https://shyentist.shinyapps.io/fish-r-man/ link. Anyone who receives this link will have not read the manual, so having a title and information about what is up top will be very helpful. And one last thought – I have recently learned about https://documentation.divio.com/ and found it to be really helpful for thinking about writing software documentation and am sharing it here in case it’s useful for you too.
Cheers, Julie
Hi @Shyentist, I have also completed my 2nd review. Nice job on revisions, you have addressed all of my comments. I particularly like the in-depth Galapagos example in the handbook (really nicely done), and that the handbook is now directly embedded in the app. I have no further edits. Best, Heather
Thank you @jules32 and @HeatherWelch for the 2nd review. I'll add an explanatory banner redirecting to the proper documentation and amend the state of the field as per suggestion. The link provided is, in fact, the one I often refer to when met with an issue with GFW data. About the documentation, thank you for Divio, I'll look into that, although I started reading {officedown}, to solve the same issue. I'll see which fares better.
Cheers 😄
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Thanks for the followup reviews @jules32 and @HeatherWelch. @jules32, that is a great documentation reference you've provided! It looks like @HeatherWelch is satisfied with the current state of the software, and @Shyentist once you've made those last changes, please let us know so that @jules32 can provide more followup comments or check off on this if the changes are sufficient.
Hi, yes, I think the paper is ready for examination @KristinaRiemer @jules32
I added the introductory message with hyperlinks and the state of the field to the best of my knowledge.
Looks good to me @Shyentist , great job 🥳
Cheers, Julie
Excellent! Thanks so much to @jules32 and @HeatherWelch for your thoughtful reviews!
@Shyentist, for next steps, I'll be proofreading and checking references of the paper (which you should feel free to do so also). After that looks good, we'll have you archive the code.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon check references
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
- 10.1002/ecs2.2753 may be a valid DOI for title: Enhancing collaboration between ecologists and computer scientists: Lessons learned and recommendations forward.
- 10.1002/ecs2.2567 may be a valid DOI for title: Evaluating the popularity of R in ecology.
INVALID DOIs
- None
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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Review checklist for @jules32
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Review checklist for @HeatherWelch
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