[REVIEW]: covid19.analytics: An R Package to Obtain, Analyze and Visualize Data from the 2019 Corona Virus Disease Pandemic

whedon commented 3 years ago

Submitting author: @mponce0 (Marcelo Ponce) Repository: https://github.com/mponce0/covid19.analytics/ Version: 2.1.0 Editor: @fboehm Reviewer: @LogIN-, @JDRomano2 Archive: 10.5281/zenodo.4640307

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Reviewer instructions & questions

@LogIN- & @JDRomano2, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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✨ 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 @LogIN-

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 (@mponce0) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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 @JDRomano2

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 (@mponce0) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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?

mponce0 commented 3 years ago

@whedon generate pdf from branch literature

whedon commented 3 years ago

Attempting PDF compilation from custom branch literature. Reticulating splines etc...

mponce0 commented 3 years ago

@mponce0 - The references need a few small fixes.

Ponce & Sandhel reference needs "R" capitalized. One way to do this is to verify that the bib file has capital R and put curly braces around the letter R. Upon compiling, this should yield a capitalized R in the references section.

The url for Smith, et al. reference needs to be fixed.

Hornik's article, in the references section, needs a capital R.

Health Canada reference - I think that it needs a capital C for Covid19. Please correct me if I'm mistaken on this.

Please make these small fixes. Once they're done, regenerate the pdf and double-check that the fixes worked. Thanks again!

@fboehm Thank you for noticing these issues, indeed there were a few references without proper "protected fields". We have fixed these and attempted recompilation via @whedon generate pdf from branch literature but it is taking an unusual long amount of time (as matter of fact it appears to be stuck...)

mponce0 commented 3 years ago

@whedon generate pdf from branch literature

whedon commented 3 years ago

Attempting PDF compilation from custom branch literature. Reticulating splines etc...

whedon commented 3 years ago

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

mponce0 commented 3 years ago

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

@fboehm the PDF compilation is working now, I think I had a bug in the references file and that's why the compilation was stalling.

fboehm commented 3 years ago

Thank you, @mponce0 . Now that your submission is ready for publication, would you please create an archive - on Figshare or Zenodo - and a new release on Github? Please report in this thread the version number for the new release and the doi for the archive. When creating the archive, please be certain to use the same title and author list (and ordering) as in the submission paper.

Here is a link to a tutorial for creating an archive: https://guides.github.com/activities/citable-code/

mponce0 commented 3 years ago

Thank you, @mponce0 . Now that your submission is ready for publication, would you please create an archive - on Figshare or Zenodo - and a new release on Github? Please report in this thread the version number for the new release and the doi for the archive. When creating the archive, please be certain to use the same title and author list (and ordering) as in the submission paper.

Here is a link to a tutorial for creating an archive: https://guides.github.com/activities/citable-code/

Many thanks @fboehm Here is the information requested:

ver: 2.1.0
Zenodo DOI: https://doi.org/10.5281/zenodo.4640307

fboehm commented 3 years ago

@whedon set version as 2.1.0

whedon commented 3 years ago

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

@whedon commands

fboehm commented 3 years ago

@whedon commands

whedon commented 3 years ago

Here are some things you can ask me to do:

# List all of Whedon's capabilities
@whedon commands

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

# Re-invite a reviewer (if they can't update checklists)
@whedon re-invite @username as reviewer

# Remove a GitHub user from the reviewers of this submission
@whedon remove @username as reviewer

# List of editor GitHub usernames
@whedon list editors

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

# Change editorial assignment
@whedon assign @username as editor

# Set the software archive DOI at the top of the issue e.g.
@whedon set 10.0000/zenodo.00000 as archive

# Set the software version at the top of the issue e.g.
@whedon set v1.0.1 as version

# Open the review issue
@whedon start review

EDITORIAL TASKS

# All commands can be run on a non-default branch, to do this pass a custom 
# branch name by following the command with `from branch custom-branch-name`.
# For example:

# Compile the paper
@whedon generate pdf

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

# Remind an author or reviewer to return to a review after a
# certain period of time (supported units days and weeks)
@whedon remind @reviewer in 2 weeks

# Ask Whedon to do a dry run of accepting the paper and depositing with Crossref
@whedon accept

# 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

EiC TASKS

# Invite an editor to edit a submission (sending them an email)
@whedon invite @editor as editor

# Reject a paper
@whedon reject

# Withdraw a paper
@whedon withdraw

# Ask Whedon to actually accept the paper and deposit with Crossref
@whedon accept deposit=true

fboehm commented 3 years ago

@whedon set 2.1.0 as version

whedon commented 3 years ago

OK. 2.1.0 is the version.

fboehm commented 3 years ago

@mponce0 - we need the title of the archive to be the same, verbatim, as that of the paper. Please change the title of the archive to: covid19.analytics: An R Package to Obtain, Analyze and Visualize Data from the 2019 Corona Virus Disease Pandemic

fboehm commented 3 years ago

@mponce0 we also need the authors list of the paper to match exactly that of the archive. Please fix this.

mponce0 commented 3 years ago

@mponce0 we also need the authors list of the paper to match exactly that of the archive. Please fix this.

@fboehm Sorry about that, I thought I have modified these items but I could see that wasn't the case... I think this time around I edited and adjusted title and authors affiliation properly. Can you please confirm this is the case?

fboehm commented 3 years ago

@mponce0 - I see that Amit Sandhel is listed as an author of the zenodo archive, yet you are the only listed author of paper.md. The two author lists need to be identical. Please fix this.

mponce0 commented 3 years ago

@fboehm I'm not sure where is this, but at the beginning of "paper.md" in the "literature" branch, https://raw.githubusercontent.com/mponce0/covid19.analytics/literature/JOSS/paper.md, we have:

---
title: 'covid19.analytics: An R Package to Obtain, Analyze and Visualize Data from the 2019 Coronavirus Disease Pandemic'
tags:
  - R
  - CRAN
  - coronavirus
  - data access
authors:
  - name: Marcelo Ponce^[corresponding author]
    orcid: 0000-0001-5850-7240
    affiliation: "1" # (Multiple affiliations must be quoted)
  - name: Amit Sandhel
    affiliation: 2
affiliations:
 - name: SciNet HPC Consortium, University of Toronto, Canada
   index: 1
 - name: Independent Researcher
   index: 2
date: 21 January 2021
bibliography: references.bib
---

Am I missing this somewhere else?

Many thanks.

mponce0 commented 3 years ago

@fboehm One more thing I forgot to mention before, as one of the reviewer noticed there was a typo in the title of our original submission, ie. instead of "Corona Virus" it should have been "Coronavirus", we fixed this in the manuscript and the Zenodo submission. Can this also be fixed in the JOSS entry?

fboehm commented 3 years ago

@whedon generate pdf from branch literature

whedon commented 3 years ago

Attempting PDF compilation from custom branch literature. Reticulating splines etc...

whedon commented 3 years ago

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

fboehm commented 3 years ago

@mponce0 - I apologize. I mistakenly thought that you were the sole author of paper.md.

fboehm commented 3 years ago

I don't think that we need to fix the JOSS issue title, where you have "Corona Virus", provided that the archive and paper pdf have the correct spelling. I'll double-check with other editors to be sure of this before we do the final acceptance. Thanks for pointing this out.

fboehm commented 3 years ago

My colleagues agreed with the above resolution.

fboehm commented 3 years ago

line 8: empowered line 14: researchers line 40: As of today line 45: Moreover, it has been reported that different line 49: This is especially line 52: As of today line 57: no comma line 63: Awkward sentence. Try "which is available on CRAN." 65: add-ons:

@mponce0 - please fix these typos.

mponce0 commented 3 years ago

@fboehm Many thanks for noticing all of these. We have gone through all and fixed them.

fboehm commented 3 years ago

@whedon generate pdf

fboehm commented 3 years ago

@whedon generate pdf from branch literature

whedon commented 3 years ago

Attempting PDF compilation from custom branch literature. Reticulating splines etc...

whedon commented 3 years ago

PDF failed to compile for issue #2995 with the following error:

Can't find any papers to compile :-(

whedon commented 3 years ago

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

fboehm commented 3 years ago

line 76: delete "sake". line 80: "of incorporating" should be "to incorporate"

Please fix these minor issues, @mponce0

mponce0 commented 3 years ago

line 76: delete "sake". line 80: "of incorporating" should be "to incorporate"

Please fix these minor issues, @mponce0

Many thanks @fboehm ! Fixed them.

mponce0 commented 3 years ago

@whedon generate pdf from branch literature

whedon commented 3 years ago

Attempting PDF compilation from custom branch literature. Reticulating splines etc...

whedon commented 3 years ago

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

fboehm commented 3 years ago

@whedon set 10.5281/zenodo.4640307 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4640307 is the archive.

fboehm commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

PDF failed to compile for issue #2995 with the following error:

Can't find any papers to compile :-(

fboehm commented 3 years ago

@whedon accept from branch literature

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1002/wics.1212 is OK
- 10.1093/nar/gkx1095 is OK
- 10.1038/d41586-020-01695-w is OK
- 10.1038/s41597-020-0524-5 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/2177

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2177, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true from branch literature

mponce0 commented 3 years ago

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

Check final proof 👉 openjournals/joss-papers#2177

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#2177, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true from branch literature 

@fboehm is this for us to take care of or the editors? In any case, many thanks for all your help and support, as well as, the referees @JDRomano2 and @LogIN-

danielskatz commented 3 years ago

This is for me, as the Associate Editor-in-Chief currently on duty. I'll proofread the paper and get back to you, probably tomorrow sometime.

openjournals / joss-reviews