[REVIEW]: 4DModeller: a spatio-temporal modelling package

[editorialbot]

Submitting author: @rwestaway (Richard Westaway)
Repository: https://github.com/4DModeller/fdmr
Branch with paper.md (empty if default branch): JOSS
Version: v0.2.0
Editor: @Nikoleta-v3
Reviewers: @PieterjanRobbe, @wcjochem
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/0f2a730dc4786def16ae43c849e07a73/status.svg)](https://joss.theoj.org/papers/0f2a730dc4786def16ae43c849e07a73)

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

@PieterjanRobbe & @wcjochem, 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 @Nikoleta-v3 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 @PieterjanRobbe

📝 Checklist for @wcjochem

[editorialbot]

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[editorialbot]

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

OK DOIs

- 10.1785/0220170246 is OK
- 10.1111/2041-210X.13168 is OK
- 10.3030/694188 is OK
- 10.1111/j.1467-9868.2008.00700.x is OK
- 10.2307/j.ctvjf9vz4 is OK
- 10.21105/joss.03914 is OK
- 10.25436/E27C7F is OK
- 10.1038/s41598-024-60964-0 is OK
- 10.1214/17-AOAS1078 is OK
- 10.1093/gji/ggac365 is OK

MISSING DOIs

- No DOI given, and none found for title: inlabru

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.08 s (743.8 files/s, 498172.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
CSV                              4              0              0          28871
Rmd                             17           1024           1364           1959
R                               21            289            532           1848
TeX                              2            110              0           1077
XML                              1              0             12            691
Markdown                         8            185              0            645
YAML                             4             11             12            210
JSON                             1              0              0              8
-------------------------------------------------------------------------------
SUM:                            58           1619           1920          35309
-------------------------------------------------------------------------------

Commit count by author:

   407	Gareth Jones
    41	Anrijs K. Abele
    40	XueqingYin
    18	mnky9800n
    12	John Aiken
     7	desireetreichler
     5	Anrijs Abele
     4	Tian Li
     3	Désirée Treichler
     2	Kristoffer Aalstad
     1	Alexander Minakov
     1	El
     1	Jonathan Bamber
     1	Julie Røste
     1	mmazzolini
     1	rwestaway

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 988

✅ 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 📄 👈

[Nikoleta-v3]

Hey all this is the review thread for the paper. All of our communications will happen here from now on.

For the reviewers, 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 #7047 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 (@Nikoleta-v3) if you have any questions/concerns. 😄 🙋🏻

[Nikoleta-v3]

I also want to bring into this issue the discussion we were having with @rwestaway.

My comment:

I see that you have some tests. Could you include some information on how to run the test suite? I really like your contribution guidelines; they are short and to the point. Maybe adding the test information there? or would be a bit much?

Whatever you decide, it would just be useful to know how to run the tests locally since the tests run when people open pull requests.

The response of:

@Nikoleta-v3 - To respond to your query, the testing suite is a relic of some old code so thank you for flagging that! At the time we had some ideas for testing meshes, and other topics, but as it stands we haven't really built it out or developed it further. However it is something planned for future work.

Thanks for clarifying. Having a test suite is not a requirement for publication with JOSS. It would be great to see some new tests being built.

Regarding the old code, I am not sure how you decided to handle this, but are you removing it? Currently it's a bit misleading.

[PieterjanRobbe]

Review checklist for @PieterjanRobbe

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/4DModeller/fdmr?
• 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 (@rwestaway) 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?

[wcjochem]

Review checklist for @wcjochem

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/4DModeller/fdmr?
• 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 (@rwestaway) 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?

[wcjochem]

Hi @rwestaway, before I get into my review, can you please clarify Contribution and Authorship for this submission (see the 'General checks' for JOSS)? I see you are not the corresponding author on the paper and you have not made substantial commits to the repository. Can you please describe your contribution to the project and this submission? Have all authors agreed to submit this work to JOSS? Thanks

[rwestaway]

Hi @wcjochem. Many thanks for agreeing to review. Please see below for author contributions based on the CRediT taxonomy – my personal contribution has been that I managed the project that produced the 4DModeller software, and I wrote the paper we submitted to JOSS. All authors (cc-ed) are happy to submit this work to JOSS. John Aiken – Investigation, Software, Methodology, Writing – review & editing, Funding acquisition Gareth Jones – Software, Methodology Xueqing Yin – Investigation, Software, Methodology Anrijs Abele – Investigation, Software, Methodology Christopher Woods – Methodology, Supervision Richard Westaway – Writing – original draft, Methodology, Project administration, Supervision Jonathan Bamber – Conceptualization, Methodology, Supervision, Writing – review & editing, Funding acquisition Please also note that I am on leave from today until 13th August. I suggest that @mnky9800n and @aabelean are the best points of contact, if needed, during that time.

[Nikoleta-v3]

Hello @wcjochem @PieterjanRobbe 👋 Any updates on your reviews? 😄

[wcjochem]

Hi @Nikoleta-v3,

Thanks for the opportunity to review this software. This project, 4Dmodeller, provides three shiny apps to support researchers applying a particular type of spatial statistical model. It does this by wrapping up and using INLA and inlabru to support a limited set of Bayesian hierarchical model forms. The R package also provides common helper functions for parsing model output, visualising data, and some useful data cleaning/conversions.

The broader project associated with the software provides a large set of "vignettes" (long-form, documentation and worked examples) that are quite valuable for anyone learning to apply these types of models. However, I note that many of those vignettes are focused on general model fitting with inlabru and INLA software and less attention is sometimes paid to the fdmr software.

I've opened a few issues with comments on the repo. My main concern is that the documentation for the functions in the package would benefit from more detail. The functions expect the parameters to be in particular forms and, which this is covered in the vignettes, it's not in the function help pages.

Regarding the manuscript, it is quite short and I don't think it currently provides a sufficient level of description particularly on the state of the field and what this software contributes to it.

At this stage, I feel I've finished my review until the authors revise the work. Thanks!

[rwestaway]

Thanks for the helpful comments @wcjochem! We will work through the issues you have opened. Regarding the manuscript length, we deliberately kept it as short as possible (it's currently ~800 words) in accordance with the JOSS submission guidelines here, but we can certainly look to include further detail on the state of the field and what the software contributes.

[PieterjanRobbe]

Hi @Nikoleta-v3, @rwestaway,

Same for me, I've started my review and opened a few issues. I'll continue my review as soon as these get resolved.

Perhaps it's also worth mentioning that I had a lot of issues installing the dependencies of 4DModeller on my M1 Mac.

Thanks!

[Nikoleta-v3]

@rwestaway, do you have any updates for us? I noticed that one of your collaborators assigned themselves to the issues raised by the reviewers two weeks ago.

[rwestaway]

Hello. Yes, @mnky9800n is coordinating our responses to the issues raised, and some have already been addressed. I know he has been pre-occupied running a workshop this week, but I believe he intends to pick it up again from next week so we'll be able to provide a better update then.

[Nikoleta-v3]

Thank you for the update!

[mnky9800n]

Hi, i added some comments on the state of the field but i am unsure how much to write there, and how exhaustive this should be. an important component of 4d-modeller is that it is an onboarding tool into the bayesian spatio-temporal modeling space. getting from 0 to somewhere in most of the packages is an exponential learning curve and we were hoping to flatten that somewhat. so the state of the field is that there isn't necessarily anyone else thinking about it in this way, to our knowledge at least.

[Nikoleta-v3]

@mnky9800n could you share a commit hash or the pull request with the changes so we can see what has been added?