[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: 1.00
Editor: @csoneson
Reviewers: @rrrlw, @MelvinSMunsaka
Archive: 10.5281/zenodo.4304831

⚠️ 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.

Status

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Markdown: [![status](https://joss.theoj.org/papers/4b7357f98bc7ac39777a7229ec30f108/status.svg)](https://joss.theoj.org/papers/4b7357f98bc7ac39777a7229ec30f108)

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

• 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 @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 🎉.

⚠️ 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.

⭐ Important ⭐

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:

2. 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]

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

[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

[rcarragh]

@whedon generate pdf

[whedon]

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

[rcarragh]

@csoneson - I've done the following:

Tagged release of software in github: 1.00
I have archived the corresponding software on Zenodo
The title and author on Zenodo match the paper; Co-author does not have an ORCID.
Zenodo archive DOI: 10.5281/zenodo.4304831

I hope this is correct, thanks.

[csoneson]

Thanks @rcarragh - could you just remove the initial rcarragh/c212 from the Zenodo record title, so that it matches the paper title? The rest looks good.

[csoneson]

@whedon set 1.00 as version

[whedon]

OK. 1.00 is the version.

[rcarragh]

Hi @csoneson,
I've removed the initial rcarragh/c212 from the Zenodo record title
Thanks

[csoneson]

@whedon set 10.5281/zenodo.4304831 as archive

[whedon]

OK. 10.5281/zenodo.4304831 is the archive.

[csoneson]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[csoneson]

Thanks @rcarragh - the associate editor-in-chief on rotation will take over from here and finalize the acceptance of your submission.

[whedon]

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

Check final proof 👉 openjournals/joss-papers#1958

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1958, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

[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

[rcarragh]

I would like to says thanks to @csoneson for organising the review process, and thanks to the reviewers, @rrrlw and @MelvinSMunsaka, for their helpful and insightful comments. Doubly so given the current difficult working conditions many are facing.

[rcarragh]

@whedon accept deposit=true

[whedon]

I'm sorry @rcarragh, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

[rcarragh]

I checked the proof and crossref in openjournals/joss-papers#1958 and they look good from my point of view.

[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:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.02706 joss-papers#1962
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02706
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...

[kyleniemeyer]

Congrats @rcarragh on your article's publication in JOSS!

Many thanks to @rrrlw and @MelvinSMunsaka for reviewing this, and @csoneson for editing it.

[whedon]

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

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.02706/status.svg)](https://doi.org/10.21105/joss.02706)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.02706/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02706/status.svg
   :target: https://doi.org/10.21105/joss.02706

This is how it will look in your documentation:

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