[REVIEW]: Vizumap: an R package for visualising uncertainty in spatial data

[whedon]

Submitting author: @lydialucchesi (Lydia Lucchesi)
Repository: https://github.com/lydialucchesi/Vizumap
Version: v1.2.0
Editor: @bstabler
Reviewers: @nuest, @GISerDaiShaoqing
Archive: 10.5281/zenodo.4554558

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Markdown: [![status](https://joss.theoj.org/papers/3caaea5389aa90e287f459bf621c8645/status.svg)](https://joss.theoj.org/papers/3caaea5389aa90e287f459bf621c8645)

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

@nuest & @GISerDaiShaoqing, 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 @bstabler know.

✨ Please try and complete your review in the next six weeks ✨

Review checklist for @nuest

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 (@lydialucchesi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @GISerDaiShaoqing

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 (@lydialucchesi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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. @bstabler 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.

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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:

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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]

Reference check summary:

OK DOIs

- 10.1002/sta4.150 is OK
- 10.1071/MF17237 is OK
- 10.1214/16-AOAS950 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

👉 Check article proof 📄 👈

[bstabler]

Hi @lydialucchesi, thanks for the submittal. This is my first review so please be patient as I learn the system. I prematurely created this issue since I'm not suppose to assign myself as both an editor and reviewer. I'm working on getting us another editor and/or reviewer. Thanks.

[bstabler]

@whedon remove @bstabler as reviewer

[whedon]

OK, @bstabler is no longer a reviewer

[bstabler]

@whedon add @nuest as reviewer

[whedon]

OK, @nuest is now a reviewer

[bstabler]

@whedon add @mikejohnson51 as reviewer

[whedon]

OK, @mikejohnson51 is now a reviewer

[nuest]

Thanks for the chance to contribute to JOSS!

I'll likely give this a go middle of next week.

[lydialucchesi]

Hi Ben, Thanks for the update and finding us several reviewers. Cheers, Lydia

…

On Tue, Jun 30, 2020 at 4:06 PM Ben Stabler ***@***.***> wrote: Hi @lydialucchesi <https://github.com/lydialucchesi>, thanks for the submittal. I goofed this up since I'm not supposed to assign myself both editor and reviewer. I'm working on getting us another editor and/or reviewer. Thanks. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2409 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE26ML7EPRXNUHS5G6JARRTRZF6F5ANCNFSM4OLXXBFA> .

[lydialucchesi]

Hi Daniel, Sounds great - thanks for letting me know. Best, Lydia

…

On Thu, Jul 2, 2020 at 6:52 PM Daniel Nüst ***@***.***> wrote: Thanks for the chance to contribute to JOSS! I'll likely give this a go middle of next week. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#2409 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AE26ML6ISPXD5NJAZBW2PETRZRDFVANCNFSM4OLXXBFA> .

[bstabler]

hi @nuest & @mikejohnson51, how's the review coming along? Thanks!

[mikejohnson51]

Hi @bstabler & @lydialucchesi,

I hope to have this done early next week if that is acceptable. Thanks!

[GISerDaiShaoqing]

@whedon generate pdf

[whedon]

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

[GISerDaiShaoqing]

Dear @lydialucchesi

Sorry to reply you late. Thanks for your revision. The authors have have done a thorough job revising the manuscript accordingly. I am satisfied with the changes made. @bstabler

Congrats on such a solid package and article.

[lydialucchesi]

Thank you for reviewing Vizumap, @GISerDaiShaoqing.

We reviewed the proofs and made a few small edits.

• Capitalised all instances of "figure"
• Changed Sub-figure B to Figure 2(B) (likewise for Figure 2(A))
• Added "for the second author" in acknowledgements
• Changed "uncertainty" to "uncertainties" in two places

@bstabler, what are the next steps in the review process?

Kind regards,
Lydia

[arfon]

@lydialucchesi - At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors

I can then move forward with accepting the submission.

[arfon]

Friendly reminder we're waiting on you to take the above next steps here @lydialucchesi before we can proceed.

[lydialucchesi]

Dear @arfon,

Thank you for your message. We have created a new release of Vizumap (v1.2.0) that includes the changes resulting from the JOSS review. We have also made an archive of the software on Zenodo. We first archived the R package on Zenodo in 2017. The latest archive for JOSS is linked to the original archive. Will that be okay?

A link to the Zenodo archive of Vizumap:
https://doi.org/10.5281/zenodo.4554558

The DOI:
10.5281/zenodo.4554558

Also, is it possible to get a copy of the most recent paper proof? We have made several small changes since the last proof was generated.

Kind regards,
Lydia

[arfon]

@whedon set 10.5281/zenodo.4554558 as archive

[whedon]

OK. 10.5281/zenodo.4554558 is the archive.

[arfon]

@whedon set v1.2.0 as version

[whedon]

OK. v1.2.0 is the version.

[arfon]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

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

OK DOIs

- 10.1002/sta4.150 is OK
- 10.1071/MF17237 is OK
- 10.1214/16-AOAS950 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

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

Check final proof 👉 openjournals/joss-papers#2105

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2105, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[arfon]

@lydialucchesi - this is the latest proof based on all the changes to date.

[lydialucchesi]

Thank you, @arfon. We have reviewed the latest proof and are happy with it. Best, Lydia

[danielskatz]

As far as I can tell, this is ready to publish but got dropped by us (JOSS) somehow, so I'm going to go ahead.

[danielskatz]

@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.02409 joss-papers#2136
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02409
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...

[danielskatz]

Congratulations to @lydialucchesi (Lydia Lucchesi) and co-authors!!

And thanks to @nuest and @GISerDaiShaoqing for reviewing, and @bstabler for editing!

[whedon]

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

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