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Reviews for the Journal of Open Source Education (JOSE)
http://jose.theoj.org
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[PRE REVIEW]: EPIDEMIC: Epidemiology Educational Code #112

Closed whedon closed 3 years ago

whedon commented 3 years ago

Submitting author: @BrunaPavlack (Bruna Silveira Pavlack) Repository: https://github.com/americocunhajr/EPIDEMIC Version: 1.0.0 Editor: @magsol Reviewers: @dalonsoa, @3mmaRand

Author instructions

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

@BrunaPavlack 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 JOSE and may be suitable for this submission.

Editor instructions

The JOSE 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 commented 3 years ago

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

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

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 commented 3 years ago 
Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.21 s (127.5 files/s, 26068.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
MATLAB                          22            677           1809           2591
Markdown                         2             71              0            262
TeX                              1              8              0             78
YAML                             2              1              4             20
-------------------------------------------------------------------------------
SUM:                            27            757           1813           2951
-------------------------------------------------------------------------------

Statistical information for the repository 'e37329ad16afc42dde04d0f3' was
gathered on 2021/05/05.
No commited files with the specified extensions were found.
whedon commented 3 years ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1101/2020.04.13.20063354 may be a valid DOI for title: SimCOVID: Open-Source Simulation Programs for the COVID-19 Outbreak
- 10.1016/j.amc.2018.06.024 may be a valid DOI for title: Calibration of a SEIR–SEI epidemic model to describe the Zika virus outbreak in Brazil
- 10.1186/1471-2105-13-76 may be a valid DOI for title: EpiFire: An open source C++ library and application for contact network epidemiology
- 10.1063/5.0005204 may be a valid DOI for title: Embedded model discrepancy: a case study of Zika modeling
- 10.4172/2155-6113.1000e107 may be a valid DOI for title: The Role of Computational Epidemiology and Risk Analysis in the Fight Against HIV/AIDS

INVALID DOIs

- None
whedon commented 3 years ago

PDF failed to compile for issue #112 with the following error: 

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:204:in `block in parse_authors': Author (Amanda Cunha Guyt) is missing affiliation (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:202:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:202:in `parse_authors'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:93:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:58:in `prepare'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'
BrunaPavlack commented 3 years ago

Suggestion from reviewers: Shannon Quinn, Juan Klopper and Erin McKiernan

labarba commented 3 years ago

@BrunaPavlack 👋 — Your paper is not compiling because the metadata is nonconforming to the specs. Please check the example paper and fix.

labarba commented 3 years ago

@whedon invite @magsol as editor

whedon commented 3 years ago

@magsol has been invited to edit this submission.

BrunaPavlack commented 3 years ago

@BrunaPavlack 👋 — Your paper is not compiling because the metadata is nonconforming to the specs. Please check the example paper and fix.

Hello! I would like help identifying what the problem is with compiling the paper. I used the site https://whedon.theoj.org/ to view and compiled it just right. Thank you very much in advance!

labarba commented 3 years ago

@openjournals/dev — We're seeing compilation errors on this submitted JOSE paper, but when I enter the repo URL and branch in the sandbox at https://whedon.theoj.org it compiles properly. Can you help us?

arfon commented 3 years ago

Author (Amanda Cunha Guyt) is missing affiliation

Please add an affiliation for Amanda Cunha Guyt as per the error above.

BrunaPavlack commented 3 years ago

Thanks for the feedback! I've already added the affiliation.

labarba 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:

magsol commented 3 years ago

@whedon assign me as editor

whedon commented 3 years ago

OK, the editor is @magsol

BrunaPavlack commented 3 years ago

Hello! Suggestion from reviewers: Shannon Quinn, Juan Klopper and Erin McKiernan

magsol commented 3 years ago

@BrunaPavlack The reviewers you suggested are excellent open science researchers, but none of them seem to have experience in computational epidemiology. Are you sure you'd like these folks to act as reviewers?

BrunaPavlack commented 3 years ago

@BrunaPavlack The reviewers you suggested are excellent open science researchers, but none of them seem to have experience in computational epidemiology. Are you sure you'd like these folks to act as reviewers?

Helo! I could not identify any with experience in the epidemiological area, feel free to suggest new reviewers.

labarba commented 3 years ago

hi @BrunaPavlack 👋 I just read your paper and I have the following comment: I miss a passage that explains to readers how they might potentially use the software in their teaching and learning context. If you have used it within a course, it helps to describe briefly how it was used. Mostly, though, what we want is to make it easier for another instructor or a self-learner to visualize how they might reuse your artifacts. Have a look at the "What should my paper contain?" of our documentation.

BrunaPavlack commented 3 years ago

Hi @labarba ! Thank you so much for the comment! We have already added in the paper the potential use of EPIDEMIC for teaching and learning. We've also added an example of using EPIDEMIC in a course on numerical and computational methods. We are available for any questions!

BrunaPavlack commented 3 years ago

Hi! I hope you are all well! Would you like to know how the review of the paper is progressing? Thank you in advance for any information!

magsol commented 3 years ago

Hi @BrunaPavlack! I'm so sorry this has been taking awhile, but I've been having a lot of trouble finding reviewers. I've been emailing potential reviewers offline, and so far have contacted 4 and had 4 subsequent declines :( I'm still following up on some additional reviewer leads, and if you have any suggestions for people who could potentially review your submission I'd be happy to hear them!

Otherwise I will certainly update you again next week with whatever progress I have made in finding reviewers.

BrunaPavlack commented 3 years ago

Hi @magsol! I understand the situation. I suggest some names of possible reviewers: rafalopespx, francocarol, vsudbrack, maxbiostat, marfcg, wcota, lsbastos, vanderfreitas, gcpeixoto and helonayala. I hope to help with suggesting these names. Thank you!

labarba commented 3 years ago

Maybe @lwjohnst86 could volunteer a review here, as the author of the recently published r-cubed paper: https://jose.theoj.org/papers/10.21105/jose.00122

magsol commented 3 years ago

Hi @BrunaPavlack! Thanks so much for the additional reviewer suggestions! I've reached out to five more (some you recommended, some others who declined to review recommended) and am hoping to hear back soon! Will update.

magsol commented 3 years ago

@whedon assign @dalonsoa as reviewer

whedon commented 3 years ago

OK, @dalonsoa is now a reviewer

magsol commented 3 years ago

@BrunaPavlack I've found one reviewer, and a possible lead on a second. Will update!

magsol commented 3 years ago

@whedon add @3mmaRand as reviewer

whedon commented 3 years ago

OK, @3mmaRand is now a reviewer

magsol commented 3 years ago

@whedon start review

whedon commented 3 years ago

OK, I've started the review over in https://github.com/openjournals/jose-reviews/issues/149.