Joss-reviews: [REVIEW]: COVID-19 Data Hub

[whedon]

Submitting author: ArdiaD (David Ardia)
Repository: https://github.com/covid19datahub/COVID19/
Version: v2.0.3
Editor: @will-rowe
Reviewers: @linuxscout, @will-rowe
Archive: 10.5281/zenodo.3939184

:warning: JOSS reduced service mode :warning:

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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/171be0f59e52bf0a4f24b76a58c55659"><img src="https://joss.theoj.org/papers/171be0f59e52bf0a4f24b76a58c55659/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/171be0f59e52bf0a4f24b76a58c55659/status.svg)](https://joss.theoj.org/papers/171be0f59e52bf0a4f24b76a58c55659)

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

@linuxscout & @mbod, 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 @will-rowe know.

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

Review checklist for @linuxscout

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (ArdiaD) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• [x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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 @will-rowe

Conflict of interest

• [x] 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

• [x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (ArdiaD) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• [x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• [x] 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?
• [x] 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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] 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. @linuxscout, @mbod it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

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.

:star: Important :star:

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:

1. 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]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/s1473-3099(20)30120-1 may be missing for title: An interactive web-based dashboard to track COVID-19 in real time

INVALID DOIs

- None

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[will-rowe]

Hey @linuxscout and @mbod - just checking in and seeing how the reviews are going. Let me know if you need anything!

[linuxscout]

Hey @will-rowe, I have defended my PhD thesis these days, I will work on review soon.

[linuxscout]

@will-rowe, I need some explanation from authors, on this feature!

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

[ArdiaD]

Hi @linuxscout; I see you've almost finished the review. Thx a lot! @mbod any chance to go over it over the coming days? thx again for your help!

[ArdiaD]

@will-rowe, I need some explanation from authors, on this feature!

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

@emanuele-guidotti what would you say here?

[ArdiaD]

Hey @linuxscout and @mbod - just checking in and seeing how the reviews are going. Let me know if you need anything!

thx @will-rowe for following up!

[ArdiaD]

@will-rowe, I need some explanation from authors, on this feature!

Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?

Hi @linuxscout. We have implemented a set of unit testing functions in the package. This is available here: https://github.com/covid19datahub/COVID19/tree/master/tests/testthat

We follow the standard practice in R, using testthat.

[linuxscout]

@ArdiaD thanks

[linuxscout]

@will-rowe I finished my review

[ArdiaD]

@will-rowe I finished my review

Thx @linuxscout for your review! This is much appreciated!

[will-rowe]

Thank you very much @linuxscout - it looks like you are happy with the submission.

[will-rowe]

@mbod - can you please let us know how you are getting on? If you are no longer able to review, please do let us know as I can sort out alternatives. I'll give you a couple of days to respond to this message

[will-rowe]

@whedon remind @will-rowe in two days

[whedon]

Reminder set for @will-rowe in two days

[ArdiaD]

@will-rowe seems like @mbod has been off for a while. Would you be kind to take over?

[will-rowe]

Yes - I'll review this today in place of @mbod

[will-rowe]

@whedon remove @mbod as reviewer

[whedon]

OK, @mbod is no longer a reviewer

[will-rowe]

@whedon add @will-rowe as reviewer

[whedon]

OK, @will-rowe is now a reviewer

[will-rowe]

@whedon generate pdf

[will-rowe]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/s1473-3099(20)30120-1 may be missing for title: An interactive web-based dashboard to track COVID-19 in real time

INVALID DOIs

- None

[ArdiaD]

@will-rowe thx a lot for taking care of that!

[will-rowe]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[will-rowe]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1016/s1473-3099(20)30120-1 may be missing for title: An interactive web-based dashboard to track COVID-19 in real time

INVALID DOIs

- None

[will-rowe]

Hey @ArdiaD - just a couple of comments for you to respond to over at the above issue

[ArdiaD]

@will-rowe all fixed! thx again for your comments!

[will-rowe]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[will-rowe]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1016/S1473-3099(20)30120-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[will-rowe]

Great - thank you for your prompt responses @ArdiaD and @emanuele-guidotti

You've addressed my comments as a reviewer, and in addition to @linuxscout's review, I think we're ready to proceed to acceptance!

As a side note, I just suggested adding a build status badge (https://github.com/covid19datahub/COVID19/pull/91), but this is not required by JOSS.

@ArdiaD - please could you now make a tagged release and archive, and report the version number and archive DOI in this thread.

[ArdiaD]

Great, thx @will-rowe

DOI is 10.5281/zenodo.3939184

Thanks!

[will-rowe]

@whedon set 0.5281/zenodo.3939184 as archive

[whedon]

0.5281/zenodo.3939184 doesn't look like an archive DOI.

[will-rowe]

@whedon set v2.0.3 as version

[whedon]

OK. v2.0.3 is the version.

[will-rowe]

@whedon set 10.5281/zenodo.3939184 as archive

[whedon]

OK. 10.5281/zenodo.3939184 is the archive.

[will-rowe]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

: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/1560

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1560, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kyleniemeyer]

Hi @ArdiaD, we are nearly done here, but I have just a few things for you to fix in the paper:

• Please put commas between the lists on page 2 (both in the Data Collection section)
• please remove either "e.g." or "etc." in the "geographic information ..." bullet on page 2; you should only have one or the other of these

Thanks!

[ArdiaD]

hi @emanuele-guidotti could you proceed?

[eguidotti]

Should be fixed now. Thanks!

[ArdiaD]

Hi @kyleniemeyer this is fixed; thx!

[kyleniemeyer]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[kyleniemeyer]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1016/S1473-3099(20)30120-1 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[whedon]

: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/1562

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1562, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kyleniemeyer]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1563
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02376
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...

[ArdiaD]

thx a lot to @linuxscout @will-rowe and @kyleniemeyer for your help in the process!

[kyleniemeyer]

Congrats @ArdiaD and @emanuele-guidotti on your article's publication in JOSS!

Many thanks to @linuxscout for reviewing this, and @will-rowe for editing/reviewing!

[whedon]

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

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.02376/status.svg)](https://doi.org/10.21105/joss.02376)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02376">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02376/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02376/status.svg
   :target: https://doi.org/10.21105/joss.02376

This is how it will look in your documentation:

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