[PRE REVIEW]: JointSurvivalModels.jl: A Julia package for Bayesian joint modeling of survival and longitudinal data

[editorialbot]

Submitting author: !--author-handle-->@ya0<!--end-author-handle-- (Yannik Ammann) Repository: https://github.com/insightsengineering/JointSurvivalModels.jl.git Branch with paper.md (empty if default branch): Version: v1.0.0 Editor: !--editor-->@RMeli<!--end-editor-- Reviewers: Pending Managing EiC: Arfon Smith

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[editorialbot]

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

OK DOIs

- 10.1093/biostatistics/kxm029 is OK
- 10.1201/b12208 is OK
- 10.1002/sim.8932 is OK
- 10.1186/s12874-020-01177-7 is OK
- 10.1002/cpt.1450 is OK
- 10.1002/sim.8756 is OK
- 10.48550/ARXIV.2011.01808 is OK
- 10.18637/jss.v072.i07 is OK
- 10.18637/jss.v084.i12 is OK
- 10.18637/jss.v071.i03 is OK
- 10.1051/0004-6361/201629272 is OK
- 10.1051/0004-6361/201322068 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1091.0 files/s, 261191.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
TOML                             7            908              2           4311
Markdown                         7            149              0            488
Julia                            6             93            157            336
TeX                              2             22              1            246
YAML                             5             17             23            122
SVG                              1              0              0             67
CSS                              1              0              1              0
-------------------------------------------------------------------------------
SUM:                            29           1189            184           5570
-------------------------------------------------------------------------------

Commit count by author:

    14  Yannik Ammann
     2  Daniel Sabanes Bove
     2  dgkf-roche
     1  Insights Engineering Bot

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 2039

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[arfon]

@editorialbot invite @RMeli as editor

:wave: @RMeli - I recognize this is somewhat outside your field, but wondered if you'd be willing to take on this submission for us?

[editorialbot]

Invitation to edit this submission sent!

[RMeli]

Hi @arfon, this is indeed quite far from my area of expertise, but if there are no better alternatives, I can take this on.

@editorialbot assign me as editor

[RMeli]

@editorialbot query scope

Hi @ya0, thank you for your submission to JOSS. This submission appears to be rather small (336 lines of code, including tests), therefore it is not clear to me that it fulfils the substantial scholarly effort criteria.

I have submitted this pre-review for editorial review. This usually takes a week or two and I'll report back here as soon as I hear back from the rest of the editorial board.

[editorialbot]

Submission flagged for editorial review.

[RMeli]

@editorialbot assign me as editor

[editorialbot]

Assigned! @RMeli is now the editor

[arfon]

Hi @ya0, thank you for your submission to JOSS. This submission appears to be rather small (336 lines of code, including tests), therefore it is not clear to me that it fulfils the substantial scholarly effort criteria.

Thanks for starting the scope review @RMeli – I managed to miss the size of this submission on initial review.

[ya0]

Thank you for looking at this poroject. @RMeli @arfon

Yes, the lines of code are low for this package, which is characteristic of the Julia ecosystem and its efficient programming language. Specifically, for scientific modeling in a Bayesian framework, we leverage Turing.jl, a top-tier Bayesian inference package, which streamlines the need for heavy interfaces and extensive code. The scholarly effort focuses on developing a concise numerical approach in Julia, capable of seamless integration with other packages in the ecosystem, and demonstrating its correctness with a practical example.

It's worth noting that the beauty of this work lies in its conciseness, showcasing an elegant solution to a complex problem. Despite exploring more code-intensive paths initially, this final design proves to be both versatile and succinct, showcasing innovation in its brevity and the use of this interface for its behavior. We anticipate relevant uptake and citations based on the compelling need for such an elegant approach, particularly in the field of clinical statistics where traditional manuscript communication remains prevalent.

[arfon]

@ya0 – thanks for this explanation. Unfortunately, after review by the JOSS editorial team we've determined that this submission doesn't meet our substantial scholarly effort criterion.

One possible alternative to JOSS is to follow GitHub's guide on how to create a permanent archive and DOI for your software. This DOI can then be used by others to cite your work.

[arfon]

@editorialbot reject

[editorialbot]

Paper rejected.