Closed whedon closed 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:.
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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.
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
And just a note to myself that we're still looking to add a reviewer directed more towards the clinical trials methodology.
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.
I have made some changes to address issues raised above: rcarragh/c212#1, rcarragh/c212#2. rcarragh/c212#3, rcarragh/c212#4.
👋 @emilydolson - could you update us on how your review is progressing?
ping @emilydolson
👋 @emilydolson - could you update us on how your review is progressing?
@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.
@whedon add @MelvinSMunsaka as reviewer
OK, @MelvinSMunsaka is now a reviewer
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
@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.
Thank you for your review @rrrlw!
👋 @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!
@MelvinSMunsaka - could you give us an update on the status of your review?
@MelvinSMunsaka - hope things are well. Could you update us on the status of your review? Thanks!
Ping @MelvinSMunsaka
@MelvinSMunsaka - hope things are well. Could you update us on the status of your review? Thanks!
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.
@csoneson - have some questions about greyed out check boxes.
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.
@whedon re-invite @MelvinSMunsaka as reviewer
OK, the reviewer has been re-invited.
@melvinsmunsaka please accept the invite by clicking this link: https://github.com/openjournals/joss-reviews/invitations
@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.
@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.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@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.
@whedon generate pdf
:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:
@MelvinSMunsaka - are you able to check the boxes in the checklist after the re-invitation?
@csoneson Yes, I just provided my responses.
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!
@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.
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.
@whedon remove @emilydolson as reviewer
OK, @emilydolson is no longer a reviewer
@whedon check references
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
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
: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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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.)
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@rrrlw & @emilydolson, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @emilydolson
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @MelvinSMunsaka
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper