[PRE REVIEW]: BART-Survival: A Bayesian machine learning approach to survival analyses in Python #7115

editorialbot · 2024-08-19T10:55:34Z

Submitting author: @twj8CDC (Jacob Tiegs)
Repository: https://github.com/CDCgov/BART-Survival
Branch with paper.md (empty if default branch):
Version: v0.1.1
Editor: @mahfuz05062
Reviewers: @turgeonmaxime, @WeakCha
Managing EiC: Kevin M. Moerman

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/f7d5279cd5936af580134d8657a1e627/status.svg)](https://joss.theoj.org/papers/f7d5279cd5936af580134d8657a1e627)

Author instructions

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The text was updated successfully, but these errors were encountered:

editorialbot · 2024-08-19T10:55:36Z

Hello human, 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:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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editorialbot · 2024-08-19T10:55:52Z

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

OK DOIs

- 10.1002/bimj.202200178 is OK
- 10.1214/19-AOS1889 is OK
- 10.1177/0962280217746191 is OK
- 10.1136/bmjopen-2023-077137 is OK
- 10.1038/s41598-020-77220-w is OK
- 10.1177/0962280218822140 is OK
- 10.18637/jss.v097.i01 is OK
- 10.1002/sim.6893 is OK
- 10.3390/stats5030038 is OK
- 10.18637/jss.v097.i01 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1136/bmj.317.7156.468 is OK
- 10.1038/sj.bjc.6601119 is OK
- 10.1214/09-AOAS285 is OK
- 10.1111/j.2517-6161.1972.tb00899.x is OK
- 10.1182/blood.V122.21.1728.1728 is OK
- 10.1007/978-3-319-19425-7 is OK
- 10.1214/08-AOAS169 is OK
- 10.1002/sim.6893 is OK
- 10.18637/jss.v097.i01 is OK

MISSING DOIs

- No DOI given, and none found for title: Bayesian Additive Regression Trees for Probabilist...
- No DOI given, and none found for title: Variable Selection with Random Survival Forest and...

INVALID DOIs

- None

editorialbot · 2024-08-19T10:55:58Z

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (591.4 files/s, 477343.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            11           3755             28          23030
SVG                              3              0              0           2689
CSS                              9            425             87           1761
JavaScript                      13            150            252            945
Python                           9            206            429            884
Jupyter Notebook                 5              0          22547            607
Markdown                        12            137              0            481
TeX                              1             22              0            342
DOS Batch                        1              8              1             26
TOML                             1              4              0             25
reStructuredText                 5             16             15             14
JSON                             1              0              0              9
make                             1              4              7              9
YAML                             1              0              0              3
-------------------------------------------------------------------------------
SUM:                            73           4727          23366          30825
-------------------------------------------------------------------------------

Commit count by author:

    56	twj8CDC
     8	dependabot[bot]
     1	Boris Ning

editorialbot · 2024-08-19T10:56:09Z

Paper file info:

📄 Wordcount for paper.md is 587

✅ The paper includes a Statement of need section

editorialbot · 2024-08-19T10:56:10Z

License info:

✅ License found: Apache License 2.0 (Valid open source OSI approved license)

editorialbot · 2024-08-19T10:56:56Z

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

editorialbot · 2024-08-19T10:57:45Z

Five most similar historical JOSS papers:

aorsf: An R package for supervised learning using the oblique random survival forest
Submitting author: @bcjaeger
Handling editor: @danielskatz (Active)
Reviewers: @danielskatz
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SurPyval: Survival Analysis with Python
Submitting author: @derrynknife
Handling editor: @dfm (Active)
Reviewers: @CamDavidsonPilon, @MatthewReid854
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BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events
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MatSurv: Survival analysis and visualization in MATLAB
Submitting author: @jhcreed
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survPen: an R package for hazard and excess hazard modelling with multidimensional penalized splines
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Handling editor: @csoneson (Active)
Reviewers: @corybrunson, @seabbs
Similarity score: 0.7205

⚠️ 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.

Kevin-Mattheus-Moerman · 2024-08-19T11:03:58Z

@twj8CDC- thanks for your submission to JOSS. Unfortunately, given the small size of this submission, it doesn't meet our substantial scholarly effort criterion. We will therefore proceed to reject this submission.

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.

Kevin-Mattheus-Moerman · 2024-08-19T11:04:09Z

@editorialbot reject

editorialbot · 2024-08-19T11:04:11Z

Paper rejected.

Kevin-Mattheus-Moerman · 2024-08-19T11:08:20Z

@twj8CDC apologies I appear to have acted too soon. I misread the above code report (looked at the number of blank lines by accident). I will work to re-open this submission. I will however query the scope as the submission is relatively small in terms of number of lines of code. So the board will review if this submission is in scope.

Kevin-Mattheus-Moerman · 2024-08-19T11:09:26Z

@openjournals/dev is there a way to "unreject" this submission? Or do the authors need to resubmit?

twj8CDC · 2024-08-19T14:20:26Z

@twj8CDC apologies I appear to have acted too soon. I misread the above code report (looked at the number of blank lines by accident). I will work to re-open this submission. I will however query the scope as the submission is relatively small in terms of number of lines of code. So the board will review if this submission is in scope.

@Kevin-Mattheus-Moerman
Hi Kevin, thanks starting the review process. If it helps, I understand the LOC is lower than normal, however we believe that we meet scientific contribution qualification based on the following factors:

There is currently no other Bayesian Additive Regression Tree (BART) for survival analysis packages ready-made in python.
The associated BART-Survival algorithm is complex enough that an applied practitioner would not be able to or would not want to implement the algorithm from scratch.
The BART-Survival algorithm is a general solution that it can be applied to most Survival modeling problems (so it is not a niche use case)

Thanks!
Jake

Kevin-Mattheus-Moerman · 2024-08-20T08:38:51Z

@openjournals/dev 👋

xuanxu · 2024-08-20T10:10:27Z

There is no editorialbot command it but I've just unrejected manually

Kevin-Mattheus-Moerman · 2024-08-20T10:17:45Z

@xuanxu great, thanks

Kevin-Mattheus-Moerman · 2024-08-20T10:18:32Z

@editorialbot query scope

editorialbot · 2024-08-20T10:18:33Z

Submission flagged for editorial review.

danielskatz · 2024-08-26T13:12:32Z

@editorialbot generate pdf

editorialbot · 2024-08-26T13:14:09Z

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

editorialbot · 2024-08-26T13:14:54Z

Five most similar historical JOSS papers:

aorsf: An R package for supervised learning using the oblique random survival forest
Submitting author: @bcjaeger
Handling editor: @danielskatz (Active)
Reviewers: @danielskatz
Similarity score: 0.7522

SurPyval: Survival Analysis with Python
Submitting author: @derrynknife
Handling editor: @dfm (Active)
Reviewers: @CamDavidsonPilon, @MatthewReid854
Similarity score: 0.7341

BayesMFSurv: An R Package to Estimate Bayesian Split-Population Survival Models With (and Without) Misclassified Failure Events
Submitting author: @Nicolas-Schmidt
Handling editor: @marcosvital (Active)
Reviewers: @alletsee, @andybega
Similarity score: 0.7265

MatSurv: Survival analysis and visualization in MATLAB
Submitting author: @jhcreed
Handling editor: @cMadan (Retired)
Reviewers: @dsurujon, @ManuelaS
Similarity score: 0.7237

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: 0.7209

⚠️ 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.

Kevin-Mattheus-Moerman · 2024-08-28T09:29:01Z

@editorialbot invite @mahfuz05062 as editor

editorialbot · 2024-08-28T09:29:04Z

Invitation to edit this submission sent!

Kevin-Mattheus-Moerman · 2024-08-28T09:37:35Z

@twj8CDC I am pleased to inform you this work passed the initial scope review. I have just invited an editor who can hopefully handle this submission. In the mean time can you work on the below:

Some editors noted your README and paper are rather terse. Could you review these, and extend them where possible. I would recommend adding a brief (nearly lay person) description of the software's purpose and applications. Next I would clearly link to the documentation and testing, it may mean having to briefly reiterate some information from the documentation, but it will make the README more complete and user friendly.
Can you try to address the potential DOI issues reported above ☝️ ? You can call @editorialbot check references to check them again. Also if you make changes to the paper you can call @editorialbot generate pdf.

twj8CDC · 2024-08-28T13:37:40Z

@Kevin-Mattheus-Moerman thats great! I will address these issues as soon as possible. Thanks!

mahfuz05062 · 2024-08-29T14:22:39Z

@editorialbot assign @mahfuz05062 as editor

editorialbot · 2024-08-29T14:22:42Z

Assigned! @mahfuz05062 is now the editor

mahfuz05062 · 2024-09-03T15:51:18Z

Hi @twj8CDC , do you have any suggestions for potential reviewers? If so, please mention them here (without tagging them with an @). You can search the list of people who have already agreed to review and may be suitable for this submission. I will then reach out to the potential reviewers to finalize the reviewers for this submission.

twj8CDC · 2024-09-04T01:51:15Z

Hi @mahfuz05062. I think L. Liu and turgeonmaxime could be potential reviewers based on their interest in Survival analysis.

How many reviewers will be selected? I can try to identify a few more if needed.

Also I am still working on updating the readme and paper per Kevins comment. I should have it updated in the next day or two.

Thanks!

mahfuz05062 · 2024-09-09T16:15:20Z

@twj8CDC We need a minimum of two reviewers to agree to review to start the review process. Also, where are you on the suggested updates/changes?

twj8CDC · 2024-09-10T16:06:55Z

@editorialbot check references

editorialbot · 2024-09-10T16:07:23Z

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

✅ OK DOIs

- 10.1002/bimj.202200178 is OK
- 10.1214/19-AOS1889 is OK
- 10.1177/0962280217746191 is OK
- 10.1136/bmjopen-2023-077137 is OK
- 10.1038/s41598-020-77220-w is OK
- 10.1177/0962280218822140 is OK
- 10.18637/jss.v097.i01 is OK
- 10.1002/sim.6893 is OK
- 10.3390/stats5030038 is OK
- 10.18637/jss.v097.i01 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1136/bmj.317.7156.468 is OK
- 10.1038/sj.bjc.6601119 is OK
- 10.1214/09-AOAS285 is OK
- 10.1111/j.2517-6161.1972.tb00899.x is OK
- 10.1182/blood.V122.21.1728.1728 is OK
- 10.1007/978-3-319-19425-7 is OK
- 10.1214/08-AOAS169 is OK
- 10.1002/sim.6893 is OK
- 10.18637/jss.v097.i01 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Bayesian Additive Regression Trees for Probabilist...
- No DOI given, and none found for title: Variable Selection with Random Survival Forest and...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

twj8CDC · 2024-09-10T16:26:04Z

@editorialbot check references

editorialbot · 2024-09-10T16:26:21Z

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

✅ OK DOIs

- 10.1002/bimj.202200178 is OK
- 10.48550/arXiv.2206.03619 is OK
- 10.1214/19-AOS1889 is OK
- 10.1177/0962280217746191 is OK
- 10.1136/bmjopen-2023-077137 is OK
- 10.1038/s41598-020-77220-w is OK
- 10.1177/0962280218822140 is OK
- 10.18637/jss.v097.i01 is OK
- 10.1002/sim.6893 is OK
- 10.3390/stats5030038 is OK
- 10.18637/jss.v097.i01 is OK
- 10.48550/arXiv.1910.02160 is OK
- 10.7717/peerj-cs.1516 is OK
- 10.1136/bmj.317.7156.468 is OK
- 10.1038/sj.bjc.6601119 is OK
- 10.1214/09-AOAS285 is OK
- 10.1111/j.2517-6161.1972.tb00899.x is OK
- 10.1182/blood.V122.21.1728.1728 is OK
- 10.1007/978-3-319-19425-7 is OK
- 10.1214/08-AOAS169 is OK
- 10.1002/sim.6893 is OK
- 10.18637/jss.v097.i01 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

twj8CDC · 2024-09-10T17:33:24Z

@mahfuz05062 I have updated the readme and paper. Everything should be ready for the review process now. Thanks!

mahfuz05062 · 2024-09-10T17:59:30Z

Hi @turgeonmaxime and @WeakCha, are you interested in reviewing this article? Thanks!

rich2355 · 2024-09-10T18:01:53Z

Sure! Best wishes, RL

…

On Tue, Sep 10, 2024 at 1:00 PM Mahfuzur Rahman ***@***.***> wrote: Hi @turgeonmaxime <https://github.com/turgeonmaxime> and @WeakCha <https://github.com/WeakCha>, are you interested in reviewing this article? Thanks! — Reply to this email directly, view it on GitHub <#7115 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ALQQQRZQ4S52USCXFGUSTBLZV4XUNAVCNFSM6AAAAABMXSPESSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGNBRGYZDGOJWHE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

turgeonmaxime · 2024-09-10T19:42:55Z

Hi @mahfuz05062 yes, I'm available and interested

mahfuz05062 · 2024-09-10T19:59:05Z

Thank you @WeakCha and @turgeonmaxime. As two reviewers agreed to perform the peer review, I will start the review process now!

mahfuz05062 · 2024-09-10T19:59:12Z

@editorialbot start review

editorialbot · 2024-09-10T19:59:14Z

Can't start a review without reviewers

mahfuz05062 · 2024-09-10T19:59:45Z

@editorialbot add @turgeonmaxime as reviewer

editorialbot · 2024-09-10T19:59:47Z

@turgeonmaxime added to the reviewers list!

mahfuz05062 · 2024-09-10T19:59:56Z

@editorialbot add @WeakCha as reviewer

editorialbot · 2024-09-10T19:59:59Z

@WeakCha added to the reviewers list!

mahfuz05062 · 2024-09-10T20:00:02Z

@editorialbot start review

editorialbot · 2024-09-10T20:00:06Z

OK, I've started the review over in #7213.

editorialbot added pre-review Track: 2 (BCM) Biomedical Engineering, Biosciences, Chemistry, and Materials labels Aug 19, 2024

editorialbot added the rejected label Aug 19, 2024

editorialbot closed this as completed Aug 19, 2024

Kevin-Mattheus-Moerman removed the rejected label Aug 19, 2024

xuanxu reopened this Aug 20, 2024

editorialbot added the query-scope Submissions of uncertain scope for JOSS label Aug 20, 2024

Kevin-Mattheus-Moerman removed the query-scope Submissions of uncertain scope for JOSS label Aug 28, 2024

editorialbot assigned mahfuz05062 Aug 29, 2024

editorialbot assigned turgeonmaxime Sep 10, 2024

editorialbot assigned rich2355 Sep 10, 2024

editorialbot closed this as completed Sep 10, 2024

[PRE REVIEW]: BART-Survival: A Bayesian machine learning approach to survival analyses in Python #7115

[PRE REVIEW]: BART-Survival: A Bayesian machine learning approach to survival analyses in Python #7115

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