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

whedon commented 3 years ago

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

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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:

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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

[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?

whedon commented 3 years ago

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 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:

csoneson commented 3 years ago

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 commented 3 years ago

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 commented 3 years ago

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

rrrlw commented 3 years ago

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 commented 3 years ago

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

csoneson commented 3 years ago

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

csoneson commented 3 years ago

ping @emilydolson

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

rcarragh commented 3 years ago

@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 commented 3 years ago

@whedon add @MelvinSMunsaka as reviewer

whedon commented 3 years ago

OK, @MelvinSMunsaka is now a reviewer

csoneson commented 3 years ago

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 commented 3 years ago

@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 commented 3 years ago

Thank you for your review @rrrlw!

csoneson commented 3 years ago

👋 @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 commented 3 years ago

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

csoneson commented 3 years ago

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

csoneson commented 3 years ago

Ping @MelvinSMunsaka

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

MelvinSMunsaka commented 3 years ago

For some reason, I am not able to add my comments via Github even after I logged into my account.

Here are my few comments:

• The articles should explain more/correctly about MedDRA and the SOC/PT in the sentence “A number of methods, which use groupings of adverse events by body-system or System Organ Class” as this is key/central to the methods presented, especially some of the Bayesian approaches.

• The reference “Fries, M., Kracht, K., & Li, J. (2016). Safety monitoring methodology in the premarketing setting. Proceedings of JSM, 2247–2269. Retrieved from https://ww2.amstat.org/MembersOnly/proceedings/2016/data/assets/pdf/389675.pdf” is incorrect. It should be “Fries, M., Kracht, K. K., Li, J., Munsaka, M. S., Sanchez-Kam, M., Singh, K. P., Wang, W., Whalen, E., Zhou. K. (2016). Safety Monitoring Methodology in the Premarketing Setting JSM 2016 Proceedings, Biopharmaceutical Section, 2247 - 2269. https://ww2.amstat.org/MembersOnly/proceedings/2016/data/assets/pdf/389675.pdf”

• I stress tested with data sets with a large number of AEs and in some cases the computations crawled to a halt, especially where using the Bayesian method. May want to mention this in the paper since in clinical trial settings the number of AEs can be very large especially in certain therapeutic areas or integrated data settings. As an FYI, we have implemented the package here: https://visual-analytics.shinyapps.io/index/ (see AE Line Plot tab) as part of the via the ASA Biopharm Safety WG ongoing work.

• In terms of the checklist above, everything checks out except for the performance issues noted above. I will complete the checklist once I can get it to work. It seems it is greyed out even when I tried changing the “watch” options.

MelvinSMunsaka commented 3 years ago

@csoneson - have some questions about greyed out check boxes.

csoneson commented 3 years ago

Thanks @MelvinSMunsaka! I will re-invite you to this issue - you have to accept the invitation in order to be able to check the boxes. Let me know if it still doesn't work.

csoneson commented 3 years ago

@whedon re-invite @MelvinSMunsaka as reviewer

whedon commented 3 years ago

OK, the reviewer has been re-invited.

@melvinsmunsaka please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations

rcarragh commented 3 years ago

@MelvinSMunsaka - thank you for your comments. I will create issues in the c212 github repository for them and respond/make changes accordingly for you to review.

rcarragh commented 3 years ago

@MelvinSMunsaka - your comments can be seen at the issues: rcarragh/c212#7, rcarragh/c212#8, rcarragh/c212#9 I will respond and let you know when I've done so.

rcarragh commented 3 years ago

@whedon generate pdf

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:

rcarragh commented 3 years ago

@whedon generate pdf

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:

rcarragh commented 3 years ago

@whedon generate pdf

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:

rcarragh commented 3 years ago

@whedon generate pdf

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:

rcarragh commented 3 years ago

@whedon generate pdf

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:

rcarragh commented 3 years ago

@whedon generate pdf

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:

rcarragh commented 3 years ago

@MelvinSMunsaka, @csoneson - I have put some responses into the issues I created for the comments (rcarragh/c212#7, rcarragh/c212#8, rcarragh/c212#9)

Briefly the following changes have been made to the paper: 1) I have added a couple of paragraphs in the Summary section explaining medical dictionaries and the motivation for the methods 2) I've fixed the reference author issue 3) I've added a section regarding performance and memory requirements in the Software Details and Availability section to give some guidance.

rcarragh commented 3 years ago

@whedon generate pdf

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:

csoneson commented 3 years ago

@MelvinSMunsaka - are you able to check the boxes in the checklist after the re-invitation?

MelvinSMunsaka commented 3 years ago

@csoneson Yes, I just provided my responses.

csoneson commented 3 years ago

Thanks @MelvinSMunsaka! It seems that you agreed with @rcarragh's changes and that the issues created in response to your comments have been closed, and all the boxes in the checklist are checked. Just to make sure I'm not missing anything, could you just confirm whether you are happy with the state of the submission now, or whether there are things that you would still like to see addressed before it should be accepted? Thanks!

MelvinSMunsaka commented 3 years ago

@csoneson I am confirming that I am happy with the state of the submission now. @rcarragh addressed all my comments. Unless there are comments from other reviewers, I would accept the submission.

csoneson commented 3 years ago

Perfect, thank you!

I have not been able to reach @emilydolson (here or via email), but given the careful reviews from @rrrlw and @MelvinSMunsaka I am happy to move on with that. @rcarragh - I will take a quick look through the submission as well and get back to you shortly.

csoneson commented 3 years ago

@whedon remove @emilydolson as reviewer

whedon commented 3 years ago

OK, @emilydolson is no longer a reviewer

csoneson commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

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