[PRE REVIEW]: MetaWards: A flexible metapopulation framework for modelling disease spread

[whedon]

Submitting author: @chryswoods (Christopher Woods) Repository: https://github.com/metawards/MetaWards Version: v1.6.1 Editor: @majensen Reviewers: @klmedeiros, @acolum Managing EiC: Kevin M. Moerman

: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.

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/417370bd5dcf72fbc9438ff8bf2f2b66"><img src="https://joss.theoj.org/papers/417370bd5dcf72fbc9438ff8bf2f2b66/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/417370bd5dcf72fbc9438ff8bf2f2b66/status.svg)](https://joss.theoj.org/papers/417370bd5dcf72fbc9438ff8bf2f2b66)

Author instructions

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

@chryswoods 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]

PDF failed to compile for issue #3840 with the following error:

 Can't find any papers to compile :-(

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.74 s (497.2 files/s, 88625.8 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                          157           6609           6052          17415
reStructuredText                108           4399           4847           9078
Cython                           40           2021           1706           5208
C                                 6            857            280           3259
C/C++ Header                      7            155             30           1535
Rmd                               5            226            187            316
Markdown                         12            119              0            300
JSON                             14              3              0            136
YAML                              2              3              6            129
Jupyter Notebook                  2              0            281             70
make                              3             30             19             69
JavaScript                        1             14              2             46
CSS                               1              9              0             37
Bourne Shell                      5             12             24             31
HTML                              2              1              0             27
Bourne Again Shell                1             11             12             25
DOS Batch                         1              0              0              3
XML                               1              0              0              2
--------------------------------------------------------------------------------
SUM:                            368          14469          13446          37686
--------------------------------------------------------------------------------

Statistical information for the repository '3f595edbac2eb23b3ef67ef7' was
gathered on 2021/10/21.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Chris Edsall                     2            63             20            0.15
Christopher Woods               92          8640           1929           19.33
Leon                            16           325            191            0.94
Leon Danon                       2           212              1            0.39
Lester Hedges                    6          2749              8            5.04
TJ McKinley                      1             6              0            0.01
chryswoods                     412         32529           7888           73.93
ellen-is                         2            64             43            0.20

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
Chris Edsall                 52           82.5         13.9               28.85
Christopher Woods         11025          127.6          9.0                5.48
Leon                       2794          859.7          1.1                7.91
Lester Hedges              2674           97.3         13.9               18.89
TJ McKinley                   6          100.0          0.9                0.00
chryswoods                19691           60.5         13.0                7.43
ellen-is                     12           18.8         15.5               25.00

[Kevin-Mattheus-Moerman]

@whedon generate pdf from branch joss

[whedon]

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

[whedon]

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

[Kevin-Mattheus-Moerman]

@whedon check references from branch joss

[whedon]

Attempting to check references... from custom branch joss

[whedon]

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

OK DOIs

- 10.1016/j.epidem.2009.11.002 is OK
- 10.1073/pnas.1000416107 is OK
- 10.1098/rstb.2020.0272 is OK
- 10.1109/mcse.2021.3083216 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[Kevin-Mattheus-Moerman]

@whedon invite @majensen as editor

[whedon]

@majensen has been invited to edit this submission.

[chryswoods]

Thanks for considering our submission. I've looked at the list of possible reviewers and maybe acolum, klmedeiros, barryrowlingson, stensy or ibontama? (I am looking at the intersection of epidemiology and python)

Thanks again for your time. Please let me know if there is anything I can do to help.

[majensen]

@whedon assign me as editor

[whedon]

OK, the editor is @majensen

[majensen]

Thanks @chryswoods - appreciate those suggestions very much!

[majensen]

@chryswoods many apologies - I have been AWOL. I will get rolling with reviewers for your work.

[majensen]

@amoeba - would you have time/interest in reviewing this work for JOSS? Much appreciated as ever -

[majensen]

@acolum - Would you have time and interest in reviewing this work for JOSS? Really appreciate your help in the past. Thanks -@majensen

[majensen]

@klmedeiros - Thanks for your previous reviews for JOSS. Would you have time and interest to review this new work? Appreciate your consideration - @majensen

[klmedeiros]

@majensen I'd be happy to!

[majensen]

@klmedeiros awesome, will add you in a jiffy

[majensen]

@whedon assign @klmedeiros as reviewer

[whedon]

OK, @klmedeiros is now a reviewer

[acolum]

@majensen Thank you, and I'd be happy to as well.

[majensen]

Wonderful @acolum!

[majensen]

@whedon add @acolum as reviewer

[whedon]

OK, @acolum is now a reviewer

[majensen]

@amoeba - thanks for considering - I have got agreement from two others, so you're off the hook for this one - MAJ

[majensen]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3914.

[majensen]

@chryswoods - thanks for your patience and @acolum @klmedeiros thanks for your service- we'll perform the review over at #3914