search

openjournals / joss-reviews

Reviews for the Journal of Open Source Software
Creative Commons Zero v1.0 Universal
703 stars 36 forks source link

[REVIEW]: 4DModeller: a spatio-temporal modelling package #7047

Open editorialbot opened 1 month ago

editorialbot commented 1 month ago

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

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0f2a730dc4786def16ae43c849e07a73"><img src="https://joss.theoj.org/papers/0f2a730dc4786def16ae43c849e07a73/status.svg"></a>
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 commented 1 month ago

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 commented 1 month ago 
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 commented 1 month ago

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 commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 988

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

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

Nikoleta-v3 commented 1 month ago

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 https://github.com/openjournals/joss-reviews/issues/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 commented 1 month ago

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 commented 1 month ago

Review checklist for @PieterjanRobbe

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

wcjochem commented 1 month ago

Review checklist for @wcjochem

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

wcjochem commented 1 month ago

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 commented 1 month ago

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 commented 1 week ago

Hello @wcjochem @PieterjanRobbe :wave: Any updates on your reviews? 😄

wcjochem commented 3 days ago

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 commented 3 days ago

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 commented 3 days ago

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!