[PRE REVIEW]: MetaCast: A package for broadCASTing epidemiological and ecological models over META-populations.

editorialbot commented 3 months ago

Submitting author: !--author-handle-->@m-d-grunnill@mstimberg<!--end-editor-- Reviewers: @acolum, @robmoss Managing EiC: Kevin M. Moerman

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d"><img src="https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d/status.svg)](https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d)

Author instructions

Thanks for submitting your paper to JOSS @m-d-grunnill. Currently, there isn't a JOSS editor assigned to your paper.

@m-d-grunnill if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

editorialbot commented 3 months ago

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

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

editorialbot commented 3 months ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.04 s (814.0 files/s, 181968.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          16            405           1270           1762
XML                              7              0              0            692
Jupyter Notebook                 1              0           2299            413
TeX                              1              5              0            169
Markdown                         2             24              0            147
TOML                             1              4              2             58
YAML                             2              7             17             28
DOS Batch                        1              8              1             26
make                             1              4              7              9
reStructuredText                 1              5              8              7
-------------------------------------------------------------------------------
SUM:                            33            462           3604           3311
-------------------------------------------------------------------------------

Commit count by author:

    61  Martin Grunnill

editorialbot commented 3 months ago

Paper file info:

📄 Wordcount for paper.md is 992

✅ The paper includes a Statement of need section

editorialbot commented 3 months ago

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot commented 3 months ago

:warning: An error happened when generating the pdf. Author (Abbas Ghasemi) is missing affiliation.

editorialbot commented 3 months ago

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

OK DOIs

- 10.18637/jss.v098.i10 is OK
- 10.21105/joss.03097 is OK
- 10.18637/jss.v104.i04 is OK
- 10.21105/joss.03247 is OK
- 10.1371/JOURNAL.PCBI.1011018 is OK
- 10.18637/jss.v098.i10 is OK
- 10.21105/joss.03539 is OK
- 10.18637/jss.v084.i08 is OK

MISSING DOIs

- 10.1101/2023.03.27.23287214 may be a valid DOI for title: Modelling Disease Mitigation at Mass Gatherings A ...
- No DOI given, and none found for title: PyGOM - A Python Package for Simplifying Modelling...
- No DOI given, and none found for title: Metapopulations
- 10.1101/2020.05.10.20097469 may be a valid DOI for title: Covasim: an agent-based model of COVID-19 dynamics...

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 3 months ago

Dear author, @m-d-grunnill, thanks for this submission. I am the AEiC on this track and here to help process the initial steps. Before we proceed, please can you have a look at the following points:

[x] Please study the above reference check :point_up: and see if you can address any of the reported potential DOI issues. You can add/amend DOI entries in your .bib file, and call @editorialbot check references here to check them again.
[x] Your project appears to lack contributing guidelines at the moment. Please work to add these and to mention/link to them in your README. You could for instance create a CONTRIBUTING.md file (see here for some examples: https://contributing.md/example/).
[x] The above paper error says:
```
gh issue comment 6571 --body ":warning: [An error happened when generating the pdf](https://github.com/openjournals/joss-papers/actions/runs/8520383968?check_suite_focus=true). Author (Abbas Ghasemi) is missing affiliation."
```
It therefore looks like the affiliation is not formatted properly. Please ensure your paper is formatted properly as per: https://joss.readthedocs.io/en/latest/submitting.html#example-paper-and-bibliography.
[ ] Please can you elaborate on the key differences/advances of this work with respect to your previous work/publication: https://doi.org/10.1371/JOURNAL.PCBI.1011018 ?

m-d-grunnill commented 3 months ago

The first 3 items of the check list have been done.

The main improvements from Grunnill et al (2024) has been to extend the framework to allow for more dimensions in the meta-population structure. The code for that project only allowed for two dimensions of meta-population structure, clusters of people and vaccination statues (as this was groupings of people we were studying).

We have also made some improvements to make the code itself more user friendly:

The sub-population function for running meta-populations can be given at initialization of MetaCaster. Previously this had to be hard coded on a child class of Base2DMetaPopModel (the old version of MetaCaster).
Dimensions of a meta-population model can be changed after initialization. This allows for easier comparison of model outputs. Base2DMetaPopModel only allowed dimensions to be set at initialization of its child classes (the old version of MetaCaster.
Instead of having two separate function for running Latin hypercube sampling in serial and parallel there is now one. This function will perform parallel simulations if given a user defined dask client. The means users can access the dask dashboard to view the progress of simulations run in parallel.
Events can be made into do nothing events via there own method. Previously this had to be done via a method of the event queue they belonged to.

Other changes made to improve users access to the code.

The code can be installed as a python package via pip.
Documentation is now available at https://metacast.readthedocs.io/en/latest/index.html
An extensive demo jupyter notebook has been made available https://github.com/m-d-grunnill/MetaCast/tree/main/demonstrations.

m-d-grunnill commented 3 months ago

Submitting author: @m-d-grunnill (Martin Grunnill) Repository: https://github.com/m-d-grunnill/MetaCast Branch with paper.md (empty if default branch): main Version: v0.1.5 Editor: Pending Reviewers: Pending Managing EiC: Kevin M. Moerman

Status

Status badge code:
HTML: <a href="https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d"><img src="https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d/status.svg)](https://joss.theoj.org/papers/ffc0f08fd3153fc487b348299810de7d)
Author instructions

Thanks for submitting your paper to JOSS @m-d-grunnill. Currently, there isn't a JOSS editor assigned to your paper.

@m-d-grunnill if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:
@editorialbot commands

Could I please suggest Rob Moss as a potential reviewer.

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot generate pdf

editorialbot commented 3 months ago

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

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot check references

editorialbot commented 3 months ago

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

OK DOIs

- 10.2307/j.ctvcm4gk0.10 is OK
- 10.18637/jss.v098.i10 is OK
- 10.48550/arXiv.1803.06934 is OK
- 10.1371/JOURNAL.PCBI.1011018 is OK
- 10.18637/jss.v094.i06 is OK
- 10.1371/journal.pcbi.1009149 is OK
- 10.21105/joss.03097 is OK
- 10.18637/jss.v104.i04 is OK
- 10.18637/jss.v084.i08 is OK
- 10.21105/joss.03539 is OK
- 10.21105/joss.03247 is OK

MISSING DOIs

- None

INVALID DOIs

- None

Kevin-Mattheus-Moerman commented 3 months ago

@m-d-grunnill thanks for the added details and fixing the above. Note that I have just flagged this for a scope review by the editorial board. This is because I need some help from the board to determine if the advancements you refer to are sufficient to warrant the new JOSS paper. This review should take about two weeks to complete.

m-d-grunnill commented 3 months ago

Just checking is it possible the submission could be considered under co-publication as outlined in https://joss.readthedocs.io/en/latest/submitting.html . Or have I misunderstood that section. Grunnill et, al. (2024) only describes a specific research use of an earlier version of the code (i.e. modelling COVID-19 at FIFA 2022). The paper I submitted outlines the software and its use more generally.

Kevin-Mattheus-Moerman commented 3 months ago

@m-d-grunnill yes that is fine. Also I can inform you that your submission has passed the initial scope check by the board. So, I will now proceed to find a handling editor.

Kevin-Mattheus-Moerman commented 3 months ago

@editorialbot invite @graciellehigino as editor

editorialbot commented 3 months ago

Invitation to edit this submission sent!

graciellehigino commented 3 months ago

Thanks for the invite, @Kevin-Mattheus-Moerman ! Unfortunately, I'm not available for editing.

Kevin-Mattheus-Moerman commented 2 months ago

Apologies @graciellehigino. Thanks for letting me know.

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot invite @lpantano as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman commented 2 months ago

@graciellehigino are you available now?

Kevin-Mattheus-Moerman commented 2 months ago

@editorialbot invite @graciellehigino as editor

editorialbot commented 2 months ago

Invitation to edit this submission sent!

graciellehigino commented 2 months ago

Hi @Kevin-Mattheus-Moerman ! I'm not editing for JOSS anymore. Sorry I don't know anyone to recommend to edit this ]=

Kevin-Mattheus-Moerman commented 2 months ago

@graciellehigino apologies, I missed that. For some reason you were back in the system and your capacity was back up too. We'll fix this. Sorry for the inconvenience.

m-d-grunnill commented 1 month ago

Any news on finding reviewers/reviewing editors? I did suggest Rob Moss as a potential reviewer earlier.

Kevin-Mattheus-Moerman commented 1 month ago

@m-d-grunnill apologies for the delays encountered so far. Because all editors in this domain are currently handling other submissions I have not been able to assign one. I've just assigned the waitlisted label so it is clear this submission should be treated once an editor becomes available. Thanks for suggesting potential reviewers. These will be useful for when a handling editor is assigned.

Kevin-Mattheus-Moerman commented 1 month ago

@m-d-grunnill I've found a handling editor! Apologies for the wait to date! Hopefully the review will now progress smoothly. Thanks for your patience!

Kevin-Mattheus-Moerman commented 1 month ago

@editorialbot assign @mstimberg as editor

editorialbot commented 1 month ago

Assigned! @mstimberg is now the editor

Kevin-Mattheus-Moerman commented 1 month ago

Thanks @mstimberg for volunteering for this one! :partying_face:

mstimberg commented 1 month ago

:wave: @m-d-grunnill I will be editing this submission, looking forward to working with you. The first step is to find reviewers, I will start doing this soon (mostly over email, so don't be surprised if you don't see much activity here for a while). I've noted your suggestion (Rob Moss) from earlier, if you have any other names you can think of, please mention them here (without directly tagging GitHub usernames with an @ to avoid spamming them). Don't hesitate to contact me (@mstimberg) in case you have any other questions or concerns.

mstimberg commented 1 month ago

@editorialbot add acolum as reviewer

editorialbot commented 1 month ago

I can't add that reviewer: acolum is not a username

mstimberg commented 1 month ago

@editorialbot add @acolum as reviewer

editorialbot commented 1 month ago

@acolum added to the reviewers list!

mstimberg commented 1 month ago

@editorialbot add @robmoss as reviewer

editorialbot commented 1 month ago

@robmoss added to the reviewers list!

mstimberg commented 1 month ago

:wave: Alright @m-d-grunnill, @acolum, and @robmoss – I am going to close this pre-review and kick off the full review which you should receive a notification for. Thanks again @acolum and @robmoss for helping out with the review!

mstimberg commented 1 month ago

@editorialbot start review

editorialbot commented 1 month ago

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6851.

openjournals / joss-reviews

[PRE REVIEW]: MetaCast: A package for broadCASTing epidemiological and ecological models over META-populations. #6571

Status

Status