Joss-reviews: [REVIEW]: c212: An R Package for the Detection of Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes)

[whedon]

Submitting author: @rcarragh (Raymond Bernard Carragher)
Repository: https://github.com/rcarragh/c212
Version: 0.98
Editor: @csoneson
Reviewers: @rrrlw, @emilydolson, @MelvinSMunsaka
Archive: Pending

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Status

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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

@rrrlw & @emilydolson, 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 @csoneson 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 @rrrlw

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 (@rcarragh) 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 @emilydolson

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

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 @MelvinSMunsaka

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

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. @rrrlw, @emilydolson 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.

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[whedon]

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

[csoneson]

Ok @rrrlw, @emilydolson - this is where the review will take place. Please find your respective checklists above together with some more instructions, and don't hesitate to ping me if you have any questions.

[whedon]

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

OK DOIs

- 10.1111/j.2517-6161.1995.tb02031.x is OK
- 10.1198/jasa.2010.tm09329 is OK
- 10.1002/sim.5310 is OK
- 10.1016/j.jspi.2007.06.006 is OK
- doi:10.1201/9781420011302.fmatt is OK
- 10.1111/j.0006-341X.2004.00186.x is OK
- 10.1080/10543406.2010.520181 is OK
- 10.1080/19466315.2017.1409134 is OK
- 10.1007/978-981-10-7826-2_11 is OK
- 10.1007/978-981-10-7826-2_11 is OK
- 10.5281/zenodo.3235282 is OK
- 10.1002/sim.8304 is OK
- 10.1002/sim.8495 is OK
- 10.1002/sim.8563 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[csoneson]

And just a note to myself that we're still looking to add a reviewer directed more towards the clinical trials methodology.

[rrrlw]

N.B. The paper has two authors and the GitHub repo has one contributor. Will trust submitting author's judgment and assume that both authors had substantial contributions and that the author list in the paper is appropriate (checking box in list above).

Edit: R package (on CRAN) has only 1 author as well.

[rcarragh]

I have made some changes to address issues raised above: rcarragh/c212#1, rcarragh/c212#2. rcarragh/c212#3, rcarragh/c212#4.

[csoneson]

👋 @emilydolson - could you update us on how your review is progressing?

[csoneson]

ping @emilydolson

👋 @emilydolson - could you update us on how your review is progressing?

[rcarragh]

@rrrlw - I've added a comment in rcarragh/c212#6 to address your question about state of the field.
I didn't close the issue so if you want to add anything further of course please do, but if you are happy with the response then we can close it.

[csoneson]

@whedon add @MelvinSMunsaka as reviewer

[whedon]

OK, @MelvinSMunsaka is now a reviewer

[csoneson]

Hi all - I'm happy to say that we now have a third reviewer - apologies for the delay and thanks a lot @MelvinSMunsaka for accepting!

Melvin - your checklist is in the first post above, and you can leave comments here and/or open issues in the software repository. Don't hesitate to ping me if you have any questions. You can also find more information about the review process here

[rrrlw]

@csoneson I have checked off all the boxes in my review. All my questions and concerns were appropriately addressed by @rcarragh in c212's GitHub repo. I should point out that although I am not qualified to review the Functionality (2nd bullet within the Functionality section), I have checked the box with the expectation that @MelvinSMunsaka will be better suited to evaluate it.

Thank you for your help, @csoneson, and thank you, @rcarragh, for this useful contribution.

[csoneson]

Thank you for your review @rrrlw!

[csoneson]

👋 @MelvinSMunsaka - I just wanted to check in to see that you have everything you need for the review, and that the practical aspects of the review process is clear. Don't hesitate to ping me if you have any questions. Thanks!

[csoneson]

@MelvinSMunsaka - could you give us an update on the status of your review?

[MelvinSMunsaka]

I will provide my review over the weekend…had some COVID-19 issues as result of getting into contact with cousin who is asymptomatic.

Also, I was taking a closer look at the package, trying out some example and also double checking how we implemented the c212 package here: (https://visual-analytics.shinyapps.io/index/ - see the AE Line Plot tab).

Melvin

From: Charlotte Soneson [e-mail]
Sent: Thursday, November 12, 2020 10:06 AM
To: openjournals/joss-reviews [e-mail]
Cc: MelvinSMunsaka [e-mail]; Mention [e-mail]
Subject: Re: [openjournals/joss-reviews] [REVIEW]: c212: An R Package for the Detection of Safety Signals in Clinical Trials Using Body-Systems (System Organ Classes) (#2706)

@MelvinSMunsaka https://github.com/MelvinSMunsaka - could you give us an update on the status of your review?

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[csoneson]

@MelvinSMunsaka - hope things are well. Could you update us on the status of your review? Thanks!