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

editorialbot commented 1 month ago

Submitting author: !--author-handle-->@melodiemonod@kanishkan91<!--end-editor-- Reviewers: Pending Managing EiC: Chris Vernon

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editorialbot commented 1 month ago

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editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (377.5 files/s, 67094.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1224           2067           4133
Markdown                         7            271              0            679
R                                7            221            158            520
TeX                              2             47              0            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           1846           3830           6410
-------------------------------------------------------------------------------

Commit count by author:

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

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1911

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

editorialbot commented 1 month ago

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

OK DOIs

- 10.1016/s0197-2456(03)00072-2 is OK
- 10.1093/bioinformatics/btr511 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

MISSING DOIs

- 10.21105/joss.01317 may be a valid DOI for title: lifelines: survival analysis in Python
- No DOI given, and none found for title: Package ‘survival’
- No DOI given, and none found for title: Pytorch: An imperative style, high-performance dee...
- No DOI given, and none found for title: scikit-survival: A Library for Time-to-Event Analy...
- No DOI given, and none found for title: Package ‘survAUC’
- 10.1109/cvpr42600.2020.00975 may be a valid DOI for title: Momentum contrast for unsupervised visual represen...
- 10.1186/s12874-018-0482-1 may be a valid DOI for title: DeepSurv: personalized treatment recommender syste...
- No DOI given, and none found for title: Time-to-Event Prediction with Neural Networks and ...
- No DOI given, and none found for title: auton-survival: An open-source package for regress...
- 10.1007/978-1-4612-4380-9_37 may be a valid DOI for title: Regression Models and Life‐Tables
- No DOI given, and none found for title: The Weibull Distribution
- No DOI given, and none found for title: A Package for Survival Analysis in R
- No DOI given, and none found for title: torchlife: Survival Analysis using pytorch
- No DOI given, and none found for title: Estimators of prediction accuracy for time-to-even...
- No DOI given, and none found for title: Time-Dependent ROC Curve and AUC for Censored Surv...
- No DOI given, and none found for title: Riskset ROC Curve Estimation from Censored Surviva...
- No DOI given, and none found for title: Time-Dependent ROC Curve Estimation from Censored ...
- No DOI given, and none found for title: Risk Regression Models and Prediction Scores for S...
- No DOI given, and none found for title: Predictive Evaluation Metrics in Survival Analysis
- No DOI given, and none found for title: Prediction Error Curves for Risk Prediction Models...

INVALID DOIs

- None

crvernon commented 1 month ago

:wave: @melodiemonod - Thanks for your submission to JOSS. While I am getting you set up with a topic editor, please see if you can fix the PDF compile issue flagged in a comment above due to their being an error in your paper or bib file. Also, please reduce the length of your paper to right around 1000 words and try to fix as many of the missing DOI listed above as you can. Thanks!

crvernon commented 1 month ago

@editorialbot invite @kanishkan91 as editor

:wave: @kanishkan91 - can you take this one on?

editorialbot commented 1 month ago

Invitation to edit this submission sent!

kanishkan91 commented 1 month ago

@crvernon I can edit this!

crvernon commented 1 month ago

@editorialbot assign @kanishkan91 as editor

editorialbot commented 1 month ago

Assigned! @kanishkan91 is now the editor

tcoroller commented 1 month ago

@editorialbot commands

editorialbot commented 1 month ago

Hello @tcoroller, here are the things you can ask me to do:


# List all available commands
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@editorialbot generate my checklist

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tcoroller commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

OK DOIs

- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.survAUC is OK
- 10.1109/cvpr42600.2020.00975 is OK
- 10.1186/s12874-018-0482-1 is OK
- 10.1007/978-1-4612-4380-9_37 is OK
- 10.1016/s0197-2456(03)00072-2 is OK
- 10.32614/CRAN.package.survival is OK
- 10.32614/CRAN.package.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

MISSING DOIs

- No DOI given, and none found for title: scikit-survival: A Library for Time-to-Event Analy...
- 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
- No DOI given, and none found for title: A Package for Survival Analysis in R

INVALID DOIs

- https://doi.org/10.21105/joss.01317 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.48550/arXiv.1912.01703 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.48550/arXiv.2204.07276 is INVALID because of 'https://doi.org/' prefix

tcoroller commented 1 month ago

@editorialbot check repository

editorialbot commented 1 month ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.18 s (370.1 files/s, 65740.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          26           1224           2067           4133
Markdown                         7            263              0            660
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           1838           3830           6411
-------------------------------------------------------------------------------

Commit count by author:

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

editorialbot commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1372

✅ The paper includes a Statement of need section

editorialbot commented 1 month ago

License info:

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

tcoroller commented 1 month ago

@editorialbot check references

editorialbot commented 1 month ago

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

MISSING 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

INVALID DOIs

- None

tcoroller commented 1 month ago

Paper file info:

📄 Wordcount for paper.md is 1372

✅ The paper includes a Statement of need section

Hi @crvernon , thank you for helping us prepare the review. I will take over the process while Melodie is away.

I have fixed the DOIs - with two that I just cannot find
I have trimmed the text to 1040 words, excluding the markdown tags (authors, affiliations) and the two table links. Please let me know if thats acceptable to you now

tcoroller commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

tcoroller commented 1 month ago

@editorialbot generate pdf

editorialbot commented 1 month ago

:warning: An error happened when generating the pdf.

tcoroller commented 1 month ago

@editorialbot generate pdf

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:

editorialbot commented 1 month ago

Five most similar historical JOSS papers:

lifelines: survival analysis in Python Submitting author: @CamDavidsonPilon Handling editor: @trallard (Retired) Reviewers: @becarioprecario, @sunhwan Similarity score: 0.6930

survxai: an R package for structure-agnostic explanations of survival models Submitting author: @AleksandraDabrowska Handling editor: @yochannah (Retired) Reviewers: @hiendn, @dirmeier Similarity score: 0.6579

survPen: an R package for hazard and excess hazard modelling with multidimensional penalized splines Submitting author: @fauvernierma Handling editor: @csoneson (Active) Reviewers: @corybrunson, @seabbs Similarity score: 0.6557

aorsf: An R package for supervised learning using the oblique random survival forest Submitting author: @bcjaeger Handling editor: @danielskatz (Active) Reviewers: @danielskatz Similarity score: 0.6373

PyMSM: Python package for Competing Risks and Multi-State models for Survival Data Submitting author: @hrossman Handling editor: @majensen (Active) Reviewers: @CamDavidsonPilon, @stefanocoretta Similarity score: 0.6355

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

crvernon commented 1 month ago

Thanks @tcoroller, @kanishkan91 will get you set up with some reviewers soon.

tcoroller commented 1 month ago

Thanks!

kanishkan91 commented 3 weeks ago

@tcoroller I was away on paternity leave. I'l make sure this review gets started in the next week. My apologies for the delay.

tcoroller commented 3 weeks ago

@kanishkan91 welcome back and thank you for the update! I came back myself recently from one, so I fully understand how busy you may be right now. Thanks again

openjournals / joss-reviews

[PRE REVIEW]: TorchSurv: A Lightweight Package for Deep Survival Analysis #7032

Status