[REVIEW]: TorchSurv: A Lightweight Package for Deep Survival Analysis

[editorialbot]

Submitting author: @melodiemonod (Mélodie Monod)
Repository: https://github.com/Novartis/torchsurv
Branch with paper.md (empty if default branch): 45-joss-submission
Version: v0.1.2
Editor: @kanishkan91
Reviewers: @WeakCha, @LingfengLuo0510
Archive: Pending

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d/status.svg)](https://joss.theoj.org/papers/02d7496da2b9cc34f9a6e04cabf2298d)

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

@WeakCha & @LingfengLuo0510, 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 @kanishkan91 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

@WeakCha, please create your checklist typing: @editorialbot generate my checklist

@LingfengLuo0510, please create your checklist typing: @editorialbot generate my checklist

[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (378.3 files/s, 67362.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1224           2070           4135
Markdown                         7            266              0            681
TeX                              2             47              0            540
R                                7            221            158            520
Jupyter Notebook                 2              0           1551            238
YAML                             6             34              6            201
TOML                             1              8              0             49
Bourne Shell                     4             20              3             40
reStructuredText                 5             16             37             13
make                             1              5              8             10
JSON                             7              0              0              7
-------------------------------------------------------------------------------
SUM:                            68           1841           3833           6434
-------------------------------------------------------------------------------

Commit count by author:

    29	Peter Krusche
    18	Thibaud Coroller
    11	corolth1
     9	melodiemonod
     7	Mélodie Monod
     2	Peter Krusche (Novartis)
     1	Ikko Eltociear Ashimine

[editorialbot]

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

✅ OK DOIs

- 10.21105/joss.01317 is OK
- 10.32614/CRAN.package.survival is OK
- 10.48550/arXiv.1912.01703 is OK
- 10.5281/zenodo.3352342 is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.1109/cvpr42600.2020.00975 is OK
- 10.1186/s12874-018-0482-1 is OK
- 10.48550/arXiv.2204.07276 is OK
- 10.1007/978-1-4612-4380-9_37 is OK
- 10.1016/s0197-2456(03)00072-2 is OK
- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.32614/CRAN.package.timeROC is OK
- 10.32614/CRAN.package.risksetROC is OK
- 10.32614/CRAN.package.survivalROC is OK
- 10.1093/bioinformatics/btr511 is OK
- 10.32614/CRAN.package.riskRegression is OK
- 10.32614/CRAN.package.SurvMetrics is OK
- 10.32614/CRAN.package.pec is OK
- 10.1111/j.0006-341x.2000.00337.x is OK
- 10.1111/j.0006-341x.2005.030814.x is OK
- 10.1002/bimj.201200045 is OK
- 10.1198/016214507000000149 is OK
- 10.1093/biostatistics/kxy006 is OK
- 10.1002/sim.4154 is OK
- 10.1002/(sici)1097-0258(19960229)15:4<361::aid-sim168>3.0.co;2-4 is OK
- 10.1002/(sici)1097-0258(19990915/30)18:17/18<2529::aid-sim274>3.0.co;2-5 is OK
- 10.1080/01621459.1977.10480613 is OK
- 10.2307/1402659 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Time-to-Event Prediction with Neural Networks and ...
- No DOI given, and none found for title: The Weibull Distribution

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1374

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[kanishkan91]

@melodiemonod, @WeakCha, @LingfengLuo0510, This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

For @WeakCha, @LingfengLuo0510 - Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

As you are probably already aware, 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 #7341 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 the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

Thanks in advance and let me know if you have any questions!!