[PRE REVIEW]: epiworldR: Fast Agent-Based Epi Models

[editorialbot]

Submitting author: !--author-handle-->@derekmeyer37<!--end-author-handle-- (Derek Meyer) Repository: https://github.com/UofUEpiBio/epiworldR Branch with paper.md (empty if default branch): paper Version: 0.0-2 Editor: !--editor-->@spholmes<!--end-editor-- Reviewers: @Abinashbunty, @carinogurjao Managing EiC: Kevin M. Moerman

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Couldn't check the bibtex because branch name is incorrect: paper

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Couldn't check the bibtex because branch name is incorrect: paper

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:warning: An error happened when generating the pdf.

[Abinashbunty]

@derekmeyer37 There is no paper branch which can be used to get the paper.md. Can you create paper branch?

[gvegayon]

@editorialbot generate pdf

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:warning: An error happened when generating the pdf.

[gvegayon]

@editorialbot generate pdf

[editorialbot]

:warning: An error happened when generating the pdf.

[gvegayon]

The last error is related to SVG figures. We have a table with SVG badges. @derekmeyer37, can you replace the SVG badges with png figures? If not, let's just write down the number of total dependencies (the second number of the badges.)

[Kevin-Mattheus-Moerman]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (563.1 files/s, 341938.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C/C++ Header                     2           4131           2432          11121
Bourne Shell                     2            458            472           3596
C++                              8            498            145           1980
R                               22            653           1702           1779
HTML                             1            120              1            680
Markdown                         5            127              0            514
Rmd                              4            167            356            168
m4                               1             31              0            145
YAML                             3             26             11             95
JSON                             2              0              0             83
TeX                              1              5              0             48
make                             1             10              0             23
-------------------------------------------------------------------------------
SUM:                            52           6226           5119          20232
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 736

[editorialbot]

Failed to discover a Statement of need section in paper

[derekmeyer37]

@editorialbot generate pdf

[editorialbot]

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

[derekmeyer37]

@editorialbot generate pdf

[editorialbot]

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

[Kevin-Mattheus-Moerman]

@derekmeyer37 thanks for this submission. I am the AEiC for this track and here to help with the initial steps. Can you confirm that the above software report featuring the lines of code counts (LOC) for the different languages is reasonably accurate? Can you clarify what encapsulates the main functionality achieved with this submission in terms of those? E.g. would it be accurate to say the core work here is centered around the ~2000 lines of R, and that the ~2k C++, and >10k C/C++ header some epiworld functionality (for which this work appears a wrapper)? Or is the C/C++ content contained herein also your personal work?

Quick note on the paper, could you add Salt Lake City, UT, United States of America, to your affiliation (assuming I got that right)? Thanks.

[derekmeyer37]

Yes, the LOC are accurate. The 11,000 lines of code is the wrapper for epiworld which we are developing as well. I also went ahead and added "Salt Lake City, UT, United States of America" to the affiliation.

[Kevin-Mattheus-Moerman]

@derekmeyer37 Thanks for that additional information. I will now proceed to find a handling editor. Note though that many are currently somewhat oversubscribed or on holiday. Hence I'll need to "waitlist" this submission for the moment and we'll have to be patient until a handling editor becomes available.

[Kevin-Mattheus-Moerman]

@spholmes this looks like it may be your cup of tea :tea:, however you are already handling several other submissions. Would you be able to let me know if you could in principle help edit this one? If so, could you let me know if you'd rather leave this waitlisted, or if we could assign this to you already. Thanks!

[spholmes]

@Kevin-Mattheus-Moerman I am happy to handle this although I am having a lot of trouble with unresponsive reviewers right now, vacations and conferences are monopolizing travel and availability. But we'll try...

[Kevin-Mattheus-Moerman]

Thanks @spholmes I'll assign you now so. I fully understand regarding the (Northern hemisphere ;) ) summer time difficulties. I am seeing extra papers as folks squeeze out a paper before going on holiday, and also many editors and reviewers are unavailable. I think it is okay to accept the longer processing times at the moment and we need not stress about it too much. There is not a lot we can do about it.

[Kevin-Mattheus-Moerman]

@editorialbot assign @spholmes as editor

[editorialbot]

Assigned! @spholmes is now the editor

[Kevin-Mattheus-Moerman]

@derekmeyer37 I have assigned an editor and formally removed the waitlisted label. However, as Susan also hinted at, our journal is experiencing a bit of a backlog and our reduced editorial force (as many are on holiday) are handling many submissions. The same issues may apply to finding reviewers, and getting them to commit to a quick review time. As such I just wanted to point out that, although we're doing our best, processing this review may take a bit longer than usual.

[Abinashbunty]

@Kevin-Mattheus-Moerman I can volunteer to review this. It is in line with my field and I have also reviewed JOSS article in the past. If you see fit, you can assign me as a reviewer.

[spholmes]

@Abinashbunty 👋 Thanks for volunteering ...I will assign you as a reviewer tonight.

[spholmes]

assign @Abinashbunty as reviewer

[spholmes]

@Abinashbunty 👋 Thanks for volunteering ...I will assign you as a reviewer tonight.

Sorry this didn't go through the way I was expecting it to...probably because I don't have another editor yet.

[spholmes]

👋 @stmcg would you be interested in reviewing this package, Thanks Susan

[spholmes]

@editorialbot assign @Abinashbunty as reviewer.

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[spholmes]

@editorialbot assign @Abinashbunty as reviewer

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I'm sorry human, I don't understand that. You can see what commands I support by typing:

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[spholmes]

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[spholmes]

@editorialbot add @Abinashbunty as reviewer

[editorialbot]

@Abinashbunty added to the reviewers list!

[stmcg]

👋 @stmcg would you be interested in reviewing this package, Thanks Susan

Thanks a lot for the invitation. This came at a particular busy time for me (am travelling very shortly) and so I won't be able to review it.

I'd suggest Carino Gurjao as a reviewer for this (carinogurjao@gmail.com). He has reviewed for JOSS before, and he'd be interested and available to review this paper

[spholmes]

Thanks Sean @stmcg for the suggestion. @carinogurjao : Would you like to review the paper on epiworldR? Many thanks

[carinogurjao]

Thank you @stmcg for suggesting me! @spholmes I'd be happy to review this paper.

[spholmes]

@editorialbot add @carinogurjao as reviewer

[editorialbot]

@carinogurjao added to the reviewers list!

[spholmes]

@editorialbot start review

[spholmes]

@editorialbot start review

[carinogurjao]

@editorialbot generate my checklist

[editorialbot]

Checklists can only be created once the review has started in the review issue

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/5781.