[PRE 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 Managing EiC: Daniel S. Katz

: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.

Author instructions

Thanks for submitting your paper to JOSS @rcarragh. Currently, there isn't an JOSS editor assigned to your paper.

@rcarragh if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

The JOSS submission bot @whedon is here to help you find and assign reviewers and start the main review. To find out what @whedon can do for you type:

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

: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.

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]

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.44 s (310.9 files/s, 98576.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                              106           3030            870          17624
C++                             14           3345           1156          14529
C/C++ Header                    14            354             45           1661
XML                              1              0              1            310
TeX                              1             33              0            271
Markdown                         1             37              0            172
-------------------------------------------------------------------------------
SUM:                           137           6799           2072          34567
-------------------------------------------------------------------------------

Statistical information for the repository '2659' was gathered on 2020/09/10.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Raymond Carragher                2         21092              2          100.00

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Raymond Carragher         21090          100.0          0.0                5.69

[whedon]

Failed to discover a valid open source license.

[whedon]

PDF failed to compile for issue #2659 with the following error:

/app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/author.rb:72:in block in build_affiliation_string': Problem with affiliations for Raymond Carragher, perhaps the affiliations index need quoting? (RuntimeError) from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/author.rb:71:ineach' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/author.rb:71:in build_affiliation_string' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/author.rb:17:ininitialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:201:in new' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:201:inblock in parse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:198:in each' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:198:inparse_authors' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon.rb:91:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/processor.rb:36:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/bin/whedon:55:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-132474d2711b/bin/whedon:119:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[whedon]

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

OK DOIs

- 10.1198/jasa.2010.tm09329 is OK
- 10.1002/sim.5310 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

- 10.2307/2346101 is INVALID
- http://dx.doi.org/10.1016/j.jspi.2007.06.006 is INVALID because of 'https://doi.org/' prefix

[danielskatz]

@rcarragh - As you can see by comments in this issue from whedon, there are some problems to be fixed.

In the repo, I see no license. I also see no README.

In the paper, you need to change the multiple affiliation line to have commas between affiliations - see https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography

You also have some extra metadata in the paper which may cause problems once the affiliations part is solved.

Finally, there are 2 DOI issues in the bib file.

Please make changes to the paper (and bib), then add @whedon generate pdf as a new comment here to regenerate the PDF. Feel free to iterate.

I will mark this as paused for now. Once you think you are ready to proceed, please tag @openjournals/joss-eics to let me (or the AEiC on duty) know.

[rcarragh]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rcarragh]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rcarragh]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rcarragh]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rcarragh]

@whedon generate pdf

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[rcarragh]

@openjournals/joss-eics

Apologies for the errors in the author affiliations section and any additional overhead caused. (I couldn't see a full compiled version through the whedon web test interface before I submitted the paper, although I could generate a pdf wth pandoc.)

I've made the following changes:

1. I have fixed the affiliations section.
2. I have added a LICENSE file to the repository.
3. I have added a README file to the repository.
4. I have updated paper.bib to address the 2 DOI issues.
5. I have removed metadata from paper.md (csl, output, header-includes)

I have been able to generate a PDF as suggested and to me it looks ok, so hopefully this has addressed the issues reported.

[danielskatz]

@whedon check references

[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

[danielskatz]

👋 @csoneson - would you be willing to edit this submission for JOSS?

[danielskatz]

@whedon invite @csoneson as editor

[whedon]

@csoneson has been invited to edit this submission.

[csoneson]

@whedon assign @csoneson as editor

[whedon]

OK, the editor is @csoneson

[csoneson]

👋 @rcarragh - I will handle this submission. Do you have any suggestions for suitable reviewers (e.g., from the spreadsheet linked in the first post above)?

Looking at your repository, it seems that you have different licenses indicated in the DESCRIPTION file and in the repository itself - could you please harmonize that? I also notice that your package doesn't seem to have any unit tests. We strongly suggest to have these; at the very least, there must be an objective way for the reviewers to verify the correct functionality of the package (see e.g. the review criteria here).

[rcarragh]

@csoneson - I will make these updates (licence and tests) and let you know when they are complete. Thanks

[rcarragh]

@whedon generate pdf

[whedon]

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

[rcarragh]

@csoneson - I have fixed the DESCRIPTION/LICENSE file issue and added a new directory to the repository called "test". This contains a README explaining the contents of the directory. The are tests for package functionality, covering all the main use cases and there are demonstration code files for the package in the subdirectory ./demo.

Starting from the bottom of the spreadsheet a couple of possible reviewers would be:

ChristopherLucas (R/C++/Bayesian statitics) emilydolson (C++/R)

but someone with a statistics/R/C++ background should be suitable.

[csoneson]

@whedon generate pdf

[whedon]

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

[csoneson]

👋 @emilydolson, @rowlandseymour, @stulacy, @rrrlw - would two of you be interested in reviewing this submission for JOSS?

c212: An R Package for the Detection of Safety Signals in Clinical Trials Using Body-Systems

[rrrlw]

I would only be able to superficially review the methodology. If a second reviewer would be willing to take that on, I’d be happy to review the software implementation.

[emilydolson]

I can review it, but I don't have any experience with clinical trial design, so I may not be the best choice (especially if the goal would be for me to focus on the methodology).

[csoneson]

Thanks @rrrlw and @emilydolson for your availability! Let me try to find a complementary third reviewer who would be more geared towards clinical trial methodology - I'll get back to you.

[rowlandseymour]

I'm in the same position as Emily. I'm happy to review it, but don't have any experience with clinical trials.

[csoneson]

👋 Just a quick update to say that I have contacted several possible reviewers on the more methodological side offline, hoping to have a positive response there.

[csoneson]

Hi again - turns out it's not so easy to find a reviewer with both clinical trial methodology expertise and free time :). I have some leads that are still open, and I will keep looking (we certainly want this aspect evaluated as well), but to avoid holding up the submission at this stage, I suggest that we start the review in the meanwhile - @rrrlw and @emilydolson, are you still available and willing to review the package (if so, @rowlandseymour, I hope we can come back to you for another submission in the future - thanks for volunteering!)

[rrrlw]

Sure, happy to help!

[emilydolson]

Me too!

[csoneson]

Brilliant, thanks both! I'll assign you and start the review issue.

[csoneson]

@whedon assign @rrrlw as reviewer

[whedon]

OK, @rrrlw is now a reviewer

[csoneson]

@whedon add @emilydolson as reviewer

[whedon]

OK, @emilydolson is now a reviewer

[csoneson]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/2706.