[REVIEW]: Mozzie: a computationally efficient simulator for the spatio-temporal modelling of mosquitoes

[editorialbot]

Submitting author: @WilkAndy (Andy Wilkins)
Repository: https://github.com/csiro-risk-assessment/mozzie
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @mengqi-z
Reviewers: @slwu89, @stulacy
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e22c754262ed8682c3f010c530917989"><img src="https://joss.theoj.org/papers/e22c754262ed8682c3f010c530917989/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e22c754262ed8682c3f010c530917989/status.svg)](https://joss.theoj.org/papers/e22c754262ed8682c3f010c530917989)

Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@emilydolson & @slwu89, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mengqi-z know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @slwu89

[editorialbot]

Hello humans, 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]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.17 s (879.6 files/s, 124303.9 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
Python                           54           1338            976           6767
CSV                              61             30              0           5561
Cython                           12            826           1159           2423
TeX                               6            171              0            888
C                                 2             38             26            478
Markdown                          3            142              0            296
Bourne Shell                      8             35              4             65
YAML                              1              1              4             25
C/C++ Header                      1             16             29             15
Bourne Again Shell                1              3             13              4
CMake                             1              0              0              4
DOS Batch                         1              0              0              1
--------------------------------------------------------------------------------
SUM:                            151           2600           2211          16527
--------------------------------------------------------------------------------

Commit count by author:

   322	WilkAndy
   106	nickbeeton
    11	Nick Beeton
     5	Keith R Hayes
     4	Maud El-Hachem
     3	ghosack
     1	Andy Wilkins

[editorialbot]

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

✅ OK DOIs

- 10.1093/femspd/fty059 is OK
- 10.1186/s12936-018-2442-y is OK
- 10.4269/ajtmh.2006.75.2_suppl.0750001 is OK
- 10.1111/1365-2664.12133 is OK
- 10.1111/2041-210X.13318 is OK
- 10.1007/s12080-022-00528-y is OK
- 10.1371/journal.pone.0297964 is OK
- 10.1371/journal.pone.0194573 is OK
- 10.1186/s12936-018-2197-5 is OK
- 10.1186/1475-2875-8-223 is OK
- 10.1016/j.mbs.2012.11.013 is OK
- 10.1016/j.camwa.2013.03.024 is OK
- 10.1016/j.matcom.2017.10.012 is OK
- 10.1371/journal.pone.0151217 is OK
- 10.1186/s13071-018-2829-1 is OK
- 10.1186/s13071-020-04426-2 is OK
- 10.1016/j.jde.2020.04.034 is OK
- 10.1007/s00285-023-02031-2 is OK
- 10.1371/journal.pcbi.1009526 is OK
- 10.1016/j.jtbi.2019.110072 is OK
- 10.1109/MCSE.2010.118 is OK
- 10.25919/2t8h-5k81 is OK
- 10.1371/journal.pcbi.1010684 is OK
- 10.1371/journal.pntd.0010863 is OK
- 10.1016/j.jmaa.2017.07.051 is OK
- 10.1038/ncomms4977 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Gaps in Globular Cluster Streams: Pal 5 and the Ga...
- No DOI given, and none found for title: Skeeter Buster: a stochastic, spatially explicit m...

❌ MISSING DOIs

- 10.1101/2023.09.09.556958 may be a valid DOI for title: MGDrivE 3: A decoupled vector-human framework for ...
- 10.1080/17513750902803588 may be a valid DOI for title: A note on the nonautonomous delay Beverton–Holt mo...

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1286

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[mengqi-z]

👋🏼 @emilydolson, @slwu89 - This is the review thread for the paper. All of our communications will happen here from now on.

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/7324 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use EditorialBot (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@mengqi-z) if you have any questions/concerns.

[WilkAndy]

Hi @nickbeeton , @hay216 , @ghosack , @maudhachem . This is where the review of our Mozzie paper will take place.

[slwu89]

Review checklist for @slwu89

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/csiro-risk-assessment/mozzie?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@WilkAndy) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[slwu89]

@mengqi-z the authors have suitably addressed my comments, and I am finished with my review.

[WilkAndy]

Thanks for your review that helped make the paper and README much better, @slwu89

[WilkAndy]

The current version of the paper is here: https://github.com/csiro-risk-assessment/mozzie/actions/runs/11357812298/artifacts/2061254076

[mengqi-z]

@slwu89 Thank you for taking the time and effort to review this submission and for completing your review so quickly!

[mengqi-z]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[mengqi-z]

👋 @emilydolson - Just checking in to see how the review is going. Could you please provide a brief status update in this thread? There's no rush, but if you anticipate any delays, please let me know. Thanks!

[mengqi-z]

👋 @emilydolson - I'm checking in on the status of your reviews. Could you please post a quick update on your progress here? Ideally, the reviews should be completed within 4-6 weeks, so if you anticipate any delays, please let me know. Thanks so much!

[mengqi-z]

👋 @emilydolson - I haven’t heard back after a few attempts to reach you, so I just wanted to confirm if you're still available to take on this review. If you've already begun, could you please share a quick update on your progress here? Thanks a lot!

[mengqi-z]

Hi @emilydolson - Since I haven’t heard back from you either here or via email, I regret to inform you that I will need to remove you from the reviewer list for this paper to keep the review process on schedule. Thank you for your understanding, and I hope you will be available to review for JOSS in the future!

[mengqi-z]

@editorialbot remove @emilydolson from reviewers

[editorialbot]

@emilydolson removed from the reviewers list!

[mengqi-z]

👋 @bramvandijk88 - I hope you're doing well. Would you be available to review a submission for JOSS? I initially reached out a while back, and you mentioned you might have availability later this fall. Unfortunately, one of our reviewers is no longer able to review, and I was hoping you could step in to fill the spot. Let me know if this works for you. Thanks!

[bramvandijk88]

👋 @bramvandijk88 - I hope you're doing well. Would you be available to review a submission for JOSS? I initially reached out a while back, and you mentioned you might have availability later this fall. Unfortunately, one of our reviewers is no longer able to review, and I was hoping you could step in to fill the spot. Let me know if this works for you. Thanks!

Hi! Sorry, I’ve overcommitted task-wise, so I’m going to have to say no. I’ll keep trying to review 1-2 submissions for JOSS every year :)

[mengqi-z]

@bramvandijk88 - Thanks for letting me know, I understand!

[mengqi-z]

👋 @martibosch @chrisvoncsefalvay - Would any of you be interested in and able to take on reviewing this JOSS submission? JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

[mengqi-z]

👋 @jGaboardi @jedalong - Would any of you be available to review this submission for JOSS? We carries out a checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[jedalong]

@mengqi-z I think i will have to say no to this as i have several other reviews ongoing atm and this is a bit too far outside of my area of expertise. J

[jGaboardi]

@mengqi-z – Also a no for me. Both the topic and the Cython codebase puts this outside my expertise.

[mengqi-z]

@jedalong @jGaboardi - No worries. Thanks for your quick reply!

[mengqi-z]

👋 @klmedeiros - Would you be interested in reviewing this submission for JOSS? We follow a check-list driven approach: https://joss.readthedocs.io/en/latest/review_criteria.html

[klmedeiros]

@mengqi-z thank you for offering, i appreciate it! unfortunately i don't know C well enough to review this the way it deserves. thanks again!

[mengqi-z]

@klmedeiros - I see! Thanks for letting me know!

[mengqi-z]

👋 @stulacy - Would you be willing to review this JOSS submission? The review process follows a check-list driven approach: https://joss.readthedocs.io/en/latest/review_criteria.html

[stulacy]

@mengqi-z Sorry, I don't have any availability before Christmas, but I'll be happy to review it in the New Year if you still need someone then.

[mengqi-z]

Hi @stulacy - I completely understand and appreciate your time. Finding reviewers has been a bit challenging, so if you’re okay with it, I’d be grateful to add you as a reviewer and follow up in the New Year. Thanks so much!

[WilkAndy]

Hi @mengqi-z , would you be OK with us suggesting reviewers? Having said this, it looks like @stulacy would be an excellent reviewer, if he's available in the New Year.

[mengqi-z]

@WilkAndy - Absolutely! Please provide the potential reviewer's GitHub username without using @ to tag them. Thanks!

[maudhachem]

@mengqi-z Here is one potential reviewer's username: MatthewKhouzam.

[mengqi-z]

👋 @MatthewKhouzam - Would you be interested in reviewing this submission for JOSS? JOSS uses a checklist-driven review process, which you can find here: https://joss.readthedocs.io/en/latest/review_criteria.html

[mengqi-z]

Hi @stulacy - Happy New Year! Just checking in to see if you're still interested and available in reviewing the submission. Thanks!

[stulacy]

Hi @mengqi-z , yep I'm still available

[mengqi-z]

@editorialbot add @stulacy as reviewer

[editorialbot]

@stulacy added to the reviewers list!

[mengqi-z]

@stulacy - That's great! Thanks so much!

Please take a moment to read the reviewer instructions at the top of this issue. Once you're ready to begin, you can start your review process by generating your review checklist using the command @editorialbot generate my checklist.