[PRE REVIEW]: individual: An R package for individual based epidemiological models

[whedon]

Submitting author: @giovannic (Giovanni Charles) Repository: https://github.com/mrc-ide/individual Version: v0.1.1 Editor: @mikldk Reviewers: @seabbs, @strengejacke, @SteRoe Managing EiC: Daniel S. Katz

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

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[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.05 s (1234.9 files/s, 145966.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               24            365            376           1734
C++                             13            148            227           1640
C/C++ Header                    12            203            125            971
TeX                              1             42              0            418
Markdown                         3             97              0            410
Rmd                              4            152            243            214
YAML                             5             32              2            150
Dockerfile                       1              4              1              9
Bourne Shell                     1              0              0              2
-------------------------------------------------------------------------------
SUM:                            64           1043            974           5548
-------------------------------------------------------------------------------

Statistical information for the repository '2b745aa89283fdf31b6e579a' was
gathered on 2021/06/16.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Giovanni                        21          1106            738           11.90
Giovanni Charles                62          6408           4758           72.04
Peter Winskill                   1            36              0            0.23
giovanni                         3           280            198            3.08
slwu89                          37          1571            405           12.75

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
Giovanni Charles           2218           34.6          7.6               10.96
slwu89                     1096           69.8          3.3               10.86

[whedon]

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

[whedon]

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

OK DOIs

- 10.1186/1471-2334-10-190 is OK
- 10.1186/s12879-017-2699-8 is OK
- 10.1146/annurev-publhealth-040617-014317 is OK
- 10.1146/annurev-statistics-010814-020218 is OK
- 10.1146/annurev-statistics-061120-034438 is OK
- 10.1016/j.tree.2012.01.014 is OK
- 10.18637/jss.v040.i08 is OK
- 10.5281/zenodo.4441210 is OK
- 10.1111/2041-210X.13286 is OK
- 10.18637/jss.v094.i06 is OK
- 10.1002/ece3.2580 is OK
- 10.18637/jss.v083.i11 is OK
- 10.1101/2021.05.13.21256216 is OK

MISSING DOIs

- 10.1007/978-0-387-33532-2_2 may be a valid DOI for title: Methods and techniques of complex systems science: An overview
- 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
- 10.1186/2194-3206-1-3 may be a valid DOI for title: Complex adaptive systems modeling with Repast Simphony
- 10.25080/majora-7b98e3ed-009 may be a valid DOI for title: MESA: an agent-based modeling framework
- 10.18637/jss.v090.i02 may be a valid DOI for title: simmer: Discrete-Event simulation for R
- 10.1111/ecog.04516 may be a valid DOI for title: NetLogoR: a package to build and run spatially explicit agent-based models in R
- 10.1016/j.epidem.2018.06.001 may be a valid DOI for title: Modeling epidemics: A primer and Numerus Model Builder implementation
- 10.1016/j.procs.2013.05.347 may be a valid DOI for title: Nova: A modern platform for system dynamics, spatial, and agent-based modeling
- 10.1101/440834 may be a valid DOI for title: SimpactCyan 1.0: An Open-source Simulator for Individual-Based Models in HIV Epidemiology with R and Python Interfaces
- 10.1177/1094342016635723 may be a valid DOI for title: Fast event-based epidemiological simulations on national scales
- 10.18637/jss.v022.i09 may be a valid DOI for title: Simecol: an object-oriented framework for ecological modeling in R
- 10.18637/jss.v084.i08 may be a valid DOI for title: EpiModel: an R package for mathematical modeling of infectious disease over networks
- 10.18637/jss.v024.i02 may be a valid DOI for title: network: a Package for Managing Relational Data in R
- 10.1109/tcss.2018.2871625 may be a valid DOI for title: Modeling Direct Transmission Diseases Using Parallel Bitstring Agent-Based Models
- 10.1016/j.idm.2017.03.001 may be a valid DOI for title: A primer on stochastic epidemic models: Formulation, numerical simulation, and analysis

INVALID DOIs

- None

[danielskatz]

@giovannic - thanks for your submission. Due to a current shortage of editors (that we are working to resolve), I'm going to put it on our waiting list until an appropriate editor is available.

[giovannic]

Potential reviewers (from bottom to top):

SteRoe nistara seabbs strengejacke

[mikldk]

@danielskatz I can edit this if you want?

[danielskatz]

Thanks @mikldk!!

Anytime you see something that's not under scope review and that you would like to edit, just take it via @whedon assign @mikldk as editor and removing the waitlisted tag if needed

[danielskatz]

@whedon assign @mikldk as editor

[whedon]

OK, the editor is @mikldk

[mikldk]

@giovannic:

• [ ] Can you please fix the missing DOI?
• [ ] Currently, the paper is too long (see the docs) -- there are lots of good material. Have you considered moving some of the material to vignettes?

[slwu89]

Hi @mikldk

I hope you don't mind me replying here; @giovannic has brilliantly led the software development but I was responsible for much of the paper text. I'll update those missing DOIs shortly.

I can shorten the paper by getting rid of all text beginning with the "Overview" on Page 4 and continuing to the end (although retaining Figure 1, which I think is quite important). I suspect though that even getting rid of 4 pages of content will still leave us above 1000 words; is a slight exceedance of that OK with the journal? I've found in the past some collaborators are reluctant to use some software if it's not accompanied by something that looks vaguely like a research article. I think keeping the sections (Summary, Statement of Need, Design Principles, and State of the Field + Figure 1) would be enough to get "buy-in" on using the software.

Also, do you have any suggestions how I can shorten the "State of the Field"? It consumes quite a bit of text because epidemic modelling has quite a few research software already (although I still think we have something new and useful to contribute).

Thanks!

[mikldk]

@slwu89 Maybe it is worth considering converting it to a preprint on e.g. arXiv? And refer to that from this JOSS paper for details?

[giovannic]

any suggestions how I can shorten the "State of the Field"?

@slwu89 I've tried to focus the "State of the Field" on R based, IBMs in Epi... https://github.com/mrc-ide/individual/pull/112

[slwu89]

@slwu89 I've tried to focus the "State of the Field" on R based, IBMs in Epi... mrc-ide/individual#112

Thanks @giovannic! That's a great help.

@mikldk would something like the tidyverse JOSS paper be an appropriate length? https://joss.theoj.org/papers/10.21105/joss.01686 I'll go through and do some further editing after we merge the edits to the "State of the Field" section https://github.com/mrc-ide/individual/pull/112

[mikldk]

@slwu89 The tidyverse paper is not the normal (...and has approx 1700 citations already). I think instead you should focus on our general guidelines: https://joss.readthedocs.io/en/latest/submitting.html#what-should-my-paper-contain

[slwu89]

Thanks @mikldk, I've done a substantial edit here (https://github.com/mrc-ide/individual/pull/113) to reduce the length of the paper to something more acceptable, as well as adding all those missing DOIs.

sample pdf

[mikldk]

@SteRoe, @nistara: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

[nistara]

Hi @mikldk, this submission looks really interesting, but it'll be difficult for me to review in a timely manner. If another reviewer is not found then I'd be happy to take this up if the authors and you don't mind a delay of more than a couple of weeks.

[mikldk]

@seabbs, @strengejacke: Would you be interested in reviewing this submission to The Journal of Open Source Software? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

[SteRoe]

Dear all,

yes, I'm interested in this review.

Best, Stefan

Am 18.07.2021 um 15:04 schrieb Mikkel Meyer Andersen:

@seabbs https://github.com/seabbs, @strengejacke https://github.com/strengejacke: Would you be interested in reviewing this submission to The Journal of Open Source Software https://joss.theoj.org/? Reviews are open and based on a checklist. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If you have any questions or concerns please let me know.

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[seabbs]

Happy to review 😄

[strengejacke]

Me too, I'd be happy to review the submission.

[mikldk]

@whedon add @seabbs as reviewer

[whedon]

OK, @seabbs is now a reviewer

[mikldk]

@whedon add @strengejacke as reviewer

[whedon]

OK, @strengejacke is now a reviewer

[mikldk]

@whedon add @SteRoe as reviewer

[whedon]

OK, @SteRoe is now a reviewer

[mikldk]

@SteRoe @seabbs @strengejacke Thanks for agreeing to review. @giovannic Thanks for the patience.

[mikldk]

@whedon check references

[whedon]

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

OK DOIs

- 10.1007/978-0-387-33532-2_2 is OK
- 10.1186/1471-2334-10-190 is OK
- 10.1186/s12879-017-2699-8 is OK
- 10.1146/annurev-publhealth-040617-014317 is OK
- 10.1146/annurev-statistics-010814-020218 is OK
- 10.1146/annurev-statistics-061120-034438 is OK
- 10.1016/j.tree.2012.01.014 is OK
- 10.18637/jss.v040.i08 is OK
- 10.1186/1471-2105-13-76 is OK
- 10.1186/2194-3206-1-3 is OK
- 10.25080/majora-7b98e3ed-009 is OK
- 10.18637/jss.v090.i02 is OK
- 10.5281/zenodo.4441210 is OK
- 10.1111/ecog.04516 is OK
- 10.1111/2041-210X.13286 is OK
- 10.1016/j.epidem.2018.06.001 is OK
- 10.1016/j.procs.2013.05.347 is OK
- 10.18637/jss.v058.i02 is OK
- 10.1093/femspd/fty059 is OK
- 10.1101/440834 is OK
- 10.1177/1094342016635723 is OK
- 10.18637/jss.v094.i06 is OK
- 10.1002/ece3.2580 is OK
- 10.18637/jss.v022.i09 is OK
- 10.18637/jss.v084.i08 is OK
- 10.18637/jss.v083.i11 is OK
- 10.18637/jss.v024.i02 is OK
- 10.1111/2041-210X.13422 is OK
- 10.1109/tcss.2018.2871625 is OK
- 10.1016/j.idm.2017.03.001 is OK
- 10.1101/2021.05.13.21256216 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[mikldk]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3539.