[PRE REVIEW]: CHIME ABM: Modeling information flow and decision making during hurricane threats

[whedon]

Submitting author: @seanbergin (Sean Bergin) Repository: https://github.com/comses/chime-abm Version: v2.0 Editor: Pending Reviewer: Pending Managing EiC: Kevin M. Moerman

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[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.

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[Kevin-Mattheus-Moerman]

@whedon generate pdf

[whedon]

PDF failed to compile for issue #3131 with the following error:

/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/orcid_validator.rb:12:in initialize': undefined methodstrip' for nil:NilClass (NoMethodError) from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:in new' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:155:inblock in check_orcids' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:in each' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:153:incheck_orcids' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon.rb:90:in initialize' from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:38:innew' 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:inprepare' 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:ininvoke_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:instart' 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:inload' from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `

'

[Kevin-Mattheus-Moerman]

@whedon check repository

[Kevin-Mattheus-Moerman]

@openjournals/dev can you help with this paper compilation error? :point_up: Thanks

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.26 s (43.1 files/s, 2900.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                              7              0              0            623
Markdown                         3             34              0             54
TeX                              1              1              0             28
-------------------------------------------------------------------------------
SUM:                            11             35              0            705
-------------------------------------------------------------------------------

Statistical information for the repository '754fbfa547985caaa9737bf1' was
gathered on 2021/03/23.
No commited files with the specified extensions were found.

[Kevin-Mattheus-Moerman]

@seanbergin thanks for this submission. I will be helping to check if this work is in scope and if needed to find handling editor. Agent based modelling is not my domain. Can you help me understand what the main "code" achievement is for this work. Would it be accurate to say it is this file: https://github.com/comses/chime-abm/blob/master/CHIME.nlogo, which appears to be about 3700 lines of nlogo and XML data, is that correct? It looks like this code is largely automatically created through the use of other software and some graphical interface, is that correct?

[seanbergin]

Kevin,

Thanks for looking at our submission so quickly. You are looking at the correct file, the CHIME.nlogo file. Netlogo does create the XML code for the user interface, but not for the actual agent based model. The XML code includes buttons, sliders and viewers to interact with the model. The actual model code is 2718 lines (including some comments at the beginning of the code) and was written by myself and the paper co-authors. It was not generated by the Netlogo program (although that would be nice).

With respect to the question of the main code achievement; the code creates a tool that researchers can use to understand the spread and interpretation of forecast information in the face of a dangerous weather event (such as a hurricane). Users can select from past hurricanes in Florida and Texas and test an array of parameters with the goal of having the right agents evacuate at the right time. The intent is to use the model to find ways to improve the hazard information system used today which has fundamentally changed so much in the last decade.

Please let me know if I can better clarify our code contribution or its purpose.

Thanks, Sean

On Tue, Mar 23, 2021 at 2:41 PM Kevin Mattheus Moerman < @.***> wrote:

@seanbergin https://github.com/seanbergin thanks for this submission. I will be helping to check if this work is in scope and if needed to find handling editor. Agent based modelling is not my domain. Can you help me understand what the main "code" achievement is for this work. Would it be accurate to say it is this file: https://github.com/comses/chime-abm/blob/master/CHIME.nlogo, which appears to be about 3700 lines of nlogo and XML data, is that correct? It looks like this code is largely automatically created through the use of other software and some graphical interface, is that correct?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3131#issuecomment-805284716, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA3324KD7RCVCIDAB7KJNQLTFEDI3ANCNFSM4ZV7LLDQ .

-- Sean Bergin Assistant Research Professor School of Complex Adaptive Systems Center for Social Dynamics & Complexity Arizona State University Tempe, AZ 85287-2402 @.***

@.***>

[Kevin-Mattheus-Moerman]

@seanbergin thanks for the clarification.

[Kevin-Mattheus-Moerman]

@whedon invite @kbarnhart as editor

[whedon]

@kbarnhart has been invited to edit this submission.

[kbarnhart]

@Kevin-Mattheus-Moerman I think it would be best if someone else could handle it. I don't have much experience with this type of model and/or software... and I'm pretty overloaded at the moment.

[kthyng]

@seanbergin I'm consulting with the editorial board to see if anyone has experience with netlogo. Thanks for your patience.

[kthyng]

@seanbergin Can your code be re-used as a library for users to input different environments to simulate hurricanes in different places? While this software is clearly useful, we're trying to suss out how much it is tied directly to this one study and related studies vs. a more general tool that other researchers would use.

Could you check out our description of how we think about publishing with JOSS alongside other publications and expand on any details we should know between your JOSS submission and your previous submissions? We particularly look for signs that the JOSS publication of the software would be its own substantial scholarly effort on top of the other publications.

[seanbergin]

Kristen,

The CHIME model can be used and modified by other users to understand hurricane evacuations in two ways. The location can be changed if the user inputs a new location (currently Florida and Texas are included)- they would need to download the appropriate GIS files on their own. The second more common way is that users can add additional storms to the model. This is something we continue to do within our own research team. On the other hand, our ABM isn't a library in the sense that one can import procedures like one might with an R package. To add a new storm or location users will have to download the necessary files, and add the new storm or location to the Netlogo menu and ABM setup procedures.

In the first publication (2017) we outlined a framework for the ABM and included a very preliminary version of the model. The second article in 2019 was more substantive. It described the potential of agent-based modeling for extreme weather events, the theoretical framework for the ABM and results related to two hurricanes. Since that publication, we worked to make the ABM useful to other researchers. This included new procedures to deal with new storm formatting from NOAA, a number of new storms, and the inclusion of census data to better inform the decisions of agents in the model. Much of our work subsequent to the 2019 article was motivated by a desire to make the CHIME ABM useful to other researchers and to expand its functionality. We believe that this represented a sizable additional effort not tied to the two previous publications.

Thank you for your time in reviewing this paper and for reaching out for clarifications. Please let me know if I can better explain anything else about the agent-based model or previous work conducted with it.

Thanks, Sean

On Fri, Apr 2, 2021 at 6:46 AM Kristen Thyng @.***> wrote:

@seanbergin https://github.com/seanbergin Can your code be re-used as a library for users to input different environments to simulate hurricanes in different places? While this software is clearly useful, we're trying to suss out how much it is tied directly to this one study and related studies vs. a more general tool that other researchers would use.

Could you check out our description https://joss.readthedocs.io/en/latest/submitting.html#co-publication-of-science-methods-and-software of how we think about publishing with JOSS alongside other publications and expand on any details we should know between your JOSS submission and your previous submissions? We particularly look for signs that the JOSS publication of the software would be its own substantial scholarly effort on top of the other publications.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/3131#issuecomment-812537783, or unsubscribe https://github.com/notifications/unsubscribe-auth/AA3324OGTVR7K3WTTDUAZJTTGXDDHANCNFSM4ZV7LLDQ .

-- Sean Bergin Assistant Research Professor School of Complex Adaptive Systems Center for Social Dynamics & Complexity Arizona State University Tempe, AZ 85287-2402 @.***

@.***>

[danielskatz]

@seanbergin - regarding the paper, please remove the blank orcid lines in the header - if there are no orcids for an author, those lines are not needed.

[seanbergin]

My co-authors forgot to include them - so I've updated the fields with their orcids. Thanks

[danielskatz]

thanks - many whedon commands can be done by anyone, like the ones I'm going to use now...

[danielskatz]

@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:

[arfon]

@seanbergin - I'm sorry to say that we're really struggling to find an editor on our team that's comfortable handling this submission as none of the team have any experience with Netlogo.

While we don't require editors to always have deep expertise in the languages of a submission being reviewed, some experience is considered normal/expected.

I will keep asking around but we may need to reject this due to our inability to review.

[arfon]

Hello @seanbergin, I'm sorry to say, we're not going to be able to review this submission at JOSS as we don't have the expertise on our editorial board to consider such a submission.

I'm going to go ahead and withdraw this submission on your behalf now.

[arfon]

@whedon withdraw

[whedon]

Paper withdrawn.