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

[editorialbot]

Submitting author: @twj8CDC (Jacob Tiegs)
Repository: https://github.com/CDCgov/BART-Survival
Branch with paper.md (empty if default branch):
Version: v.0.1.1
Editor: @mahfuz05062
Reviewers: @turgeonmaxime, @rich2355
Archive: 10.5281/zenodo.14105188

Status

Status badge code:

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

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

@turgeonmaxime & @WeakCha, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @mahfuz05062 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 @turgeonmaxime

📝 Checklist for @WeakCha

📝 Checklist for @rich2355

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (603.6 files/s, 482772.9 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
XML                              1              0              0            718
Markdown                        12            238              0            696
Jupyter Notebook                 5              0          22547            607
TeX                              1             22              0            344
YAML                             2              1              4             27
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
-------------------------------------------------------------------------------
SUM:                            75           4829          23370          31784
-------------------------------------------------------------------------------

Commit count by author:

   108	twj8CDC
     8	dependabot[bot]
     1	Boris Ning

[editorialbot]

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

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1637

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[mahfuz05062]

@turgeonmaxime and @WeakCha - Thank you for agreeing to review this submission.

This is the review thread for the paper. All of our communications will happen here from now on.

As mentioned above, you can use the command @editorialbot generate my checklist to create your review checklist. 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 (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html)

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #7213 so that a link is created to this thread for visibility. 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 you require additional time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period.

Please feel free to ping me (@mahfuz05062) if you have any questions/concerns.

[rich2355]

Review checklist for @WeakCha

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/CDCgov/BART-Survival?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@twj8CDC) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[rich2355]

Thanks for inviting me for reviewing this paper and I like the idea of extending BART from R to Python. I have taken a quick overview of the paper and the software and I have these comments.

For the paper:

1. In line 64, please remove the parentheses around j = 1, ..., k.
2. In line 63-68, it would be great to have a small example explaining how to calculate P_{t_j}, just like you did in the later part of this paper.
3. In line 71-72, I understand that x_i should be the observation i, but please indicate that (and also other similar math notations) explicitly and clearly.
4. In line 83-85, it would be great to give another example with event status = 0, as people may not easily obtain the sequence for this case. Also, your example in the paper is wrong because the event time 14 is missing.
5. In line 93, it is good to explain the meaning of the two parameters of BART. Also, the meaning of \Phi should be pointed out explicitly, although people in stats should know that this is the CIF of the normal distribution.
6. The goal of the inference section looks unclear to me. Again, it would be great to have examples show how to construct a APD dataset, and how to compute marginal difference, marginal risk ratio, etc. with a real dataset. Also, some sentences look confusing to me. For example, what is the meaning of "Here j_{T_max} is the maximum time across all event times."?
7. Following 6, please indicate the meaning of E_i and E_{ij}. They are expectations over which variable, and how to calculate them empirically?
8. You mentioned credible interval in Bayesian statistics, which is great. But could you explain how to calculate that in your software? Use which function? This could be complemented by a data example, which I also commented below.
9. A code example for running a simple dataset is missing. I found it in your Github but I think it should also be available in your paper explaining the usages and the results that you get from your software.
10. Have you tried comparing your BART-survival with the version in R? I did not find evidence in your paper, just wanna ask whether we could verify your implementation.

For the software:

1. The links to User Guide/Example Notebooks are not working.
2. You used the word "SV" a lot of times in your example1.ipynb. Does that mean "survival"?

I may give more comments when I have chance to test this software on my PC, but in general, the idea is interesting, although some refinement may be needed.

Please feel free to let me know if you have any questions, or correct me if I am wrong, thanks!

[twj8CDC]

@WeakCha
Thank you for the initial round of edits. I will work on updating based on these comments.

As far as point 10. We did do an extensive validation analysis for our method with simulations and real data, in which we compared our algorithm to the R based algorithm. However, I was under the impression that JOSS did not necessarily want this type of analysis in the JOSS papers. We were planning to put together the validation study in a separate paper.

I could provide an example comparing our algorithm and the R algorithm using a simulated dataset if you think that would be sufficient. Or if you have other thoughts?

[rich2355]

@twj8CDC Thank you for the reply and you mentioned a good point. Regardless of any preference of JOSS I would simply add a few sentences saying something like "based on our evaluation test, our software successfully reproduces the functionalities in the R version". But I have no idea about this kind of preference. @mahfuz05062 Do you have thoughts on this?

If this is not necessarily shown on JOSS, you do not need to modify anything on the paper. But it would be great if you could provide an example of comparison, and put these comparison code in your github example folder. (could be a py file with the compared R code commented out)

Definitely open to other thoughts!

[turgeonmaxime]

Review checklist for @turgeonmaxime

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/CDCgov/BART-Survival?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@twj8CDC) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[mahfuz05062]

@WeakCha and @twj8CDC, I don't think an extensive analysis is necessary here but I like the idea mentnioned by @twj8CDC "comparing our algorithm and the R algorithm using a simulated dataset". If you can provide something like this, it should be sufficient.

[twj8CDC]

@mahfuz05062 sounds great, I will add an example of this sort to the paper.
@WeakCha additionally, I have addressed most of the other revisions suggested. I will have a new revised paper uploaded in the next day or two. Thanks!

[rich2355]

Hi @twj8CDC ! Out of curiosity, have you generated the PDF for us to further review?

[twj8CDC]

Hi @WeakCha. Sorry for the delay, but yes I did just update the pdf! Thanks

[twj8CDC]

@editorialbot generate pdf

[editorialbot]

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

[rich2355]

@mahfuz05062 @twj8CDC Thank you so much for editing your paper, I agree that your paper looks much better! Here is a list of my new comments:

1. In line 72, typically [] means inclusive while () means exclusive.
2. In line 139, 8 * 6 = 48 not 36.
3. In line 294, the link for comparing your algorithm to the R version does not work.

I will take a look at the github repo soon and will get back to you if I have more comments. Thanks a lot for your editing, I think the paper now is much richer and more detailed!

[rich2355]

@twj8CDC Hi, I come back for the GitHub repo! For your Github repo,

1. The theoretical background for your software paper does not need to be put in your README, as people interested in your software usage typically will spend little time understanding theories.
2. In the README, in the section User Guide/Example Notebooks, the two links are not working.
3. Your example notebooks look detailed, and easy to follow. And I like it! But please explain the meaning of the abbreviation "SV", so that readers will not feel confused.
4. There are many warning messages in your notebooks, and I would recommend removing most of them for better readability. However, it is optional because I know some warning messages are not easy to be removed...

[mahfuz05062]

Hi @twj8CDC, can you make necessary change according to the suggestions from @WeakCha ?

[mahfuz05062]

@turgeonmaxime I haven't seen much activity from your side. Is there anything that I can help with or do you need more time?

[twj8CDC]

@mahfuz05062 Yes I will complete these changes over the next couple days! Thanks

[turgeonmaxime]

@turgeonmaxime I haven't seen much activity from your side. Is there anything that I can help with or do you need more time?

Sorry @mahfuz05062, I've been busy with work, but I'm actually reading the newest version right now! I should have some comments to share later today.

[turgeonmaxime]

@twj8CDC Thanks for your updates to the paper. I think one crucial point that is still lacking from the manuscript is what role BART-Survival fulfills that PyMC-BART doesn't. Based on my reading of the manuscript but also pre-review discussions here on Github, generating the datasets required for the analysis is a non-trivial task. You should write this explicitly in the text. It is the main message.

Similarly, I think you did a good job explaining the need for BART-Survival when a similar R package already exists. And that's also a crucial requirement, so thanks for that.

Beyond that, I have a few more comments, some general and some more targeted:

• In general, it is recommended to use punctuation with equations, as they are generally part of a sentence. For example, on line 81, the equation should end with a comma, and the equation on line 82 should end with a period. Moreover, if you add extra context after an equation (e.g. line 185), the equation above should end with a comma and the sentence that follows should start with a small letter (i.e. "where" instead of "Where").
• Related to the comment above, it would be awkward to try and do the same with the tables that are part of your sentences (e.g. lines 69 and 71), so I think it's fine to drop the punctation in those cases. I would therefore recommend rephrasing line 72 so that you get a complete sentence. For example, "In the table above, the intervals are..."
• I'm not sure why "Survival" appears multiple times with a capital S. Please review and fix as needed.
• What you describe as the "simple setting" in the "Background" subsection is essentially the Kaplan-Meier non-parametric estimator. I would suggest you add that clarification and maybe also a reference to your favourite textbook on survival analysis.
• L124: More generally, the dataset TAD can be used for binary regression. Probit regression is just one type of binary regression.
• L147: PAD length should be 48 (which was also mentioned by @WeakCha).
• L161: Typo, "the of the probability"
• L201: Missing a period at the end of the sentence.
• L235: The sentence should be reviewed, I think it should be "These expectations can be further used to make comparisons can be made between".
• L265: what are the weights and coords parameters?
• L268: I think it should be a small s in "The p,S arrays..."
• L294: There is a typo in the URL, hence why the link doesn't work.

I'll have a look at the repo itself and report back.

[turgeonmaxime]

@twj8CDC One more thing: could you add a short description of the rossi dataset that you used for the demonstration. Just a sentence or two would be helpful (especially since the lifelines documentation doesn't even mention what the "survival" event is).

[editorialbot]

Done! version is now v.0.1.1

[mahfuz05062]

@editorialbot generate pdf

[editorialbot]

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

[rich2355]

@editorialbot generate checklist

[editorialbot]

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@editorialbot commands

[rich2355]

Review checklist for @rich2355

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/CDCgov/BART-Survival?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@twj8CDC) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1. Contribute to the software 2. Report issues or problems with the software 3. Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[rich2355]

@mahfuz05062 Done!

[mahfuz05062]

@editorialbot generate pdf

[editorialbot]

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

[mahfuz05062]

@editorialbot remove WeakCha from reviewers

[editorialbot]

I can't add that reviewer: WeakCha is not a username

[mahfuz05062]

@editorialbot remove @WeakCha from reviewers

[editorialbot]

@WeakCha removed from the reviewers list!

[mahfuz05062]

@editorialbot generate pdf

[editorialbot]

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

[mahfuz05062]

@editorialbot check references

[editorialbot]

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
- 10.1159/000324758 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

- No DOI given, and none found for title: Money, Work, and Crime: Some Experimental Results

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[mahfuz05062]

@mahfuz05062 Done!

Thanks! I removed your old name from reviewers list. We should be good now.

[mahfuz05062]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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
- 10.1159/000324758 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

- No DOI given, and none found for title: Money, Work, and Crime: Some Experimental Results

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/bcm-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#6282, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[twj8CDC]

Hi @mahfuz05062,

Do you know how long it typically take for the publication process to be finalized?
There are no final steps required from my end correct?

Thanks
Jake

[mahfuz05062]

Hi @mahfuz05062,

Do you know how long it typically take for the publication process to be finalized? There are no final steps required from my end correct?

Thanks Jake

@twj8CDC I have seen the finalization process to be completed within 1-2 weeks. However, as the last couple of weeks were holidays, it may be slower than usual. The next step is the track editor will go through the article and may provide some suggestions for modification, and then officially approve the publication. But, yes, you don't have anything to do until then.

[Kevin-Mattheus-Moerman]

@twj8CDC as AEiC for JOSS I will now help to process this submission for acceptance in JOSS. Below are some final checks, some of which may require your attention:

Checks on repository

• Project has OSI approved license
• Project features contributing guidelines

Checks on review issue

• Review completed
• Software version tag listed here matches a tagged release

Checks on archive

• Archive listed title and authors matches paper
• Archive listed license matches software license
• Archive listed version tag matches tagged release (and includes a potential v).

Checks on paper

• Checked paper formatting
• Check affiliations to make sure country acronyms are not used
• Checked reference rendering
• Checked if pre-print citations can be updated by published versions
• Checked for typos

Remaining points:

As you can see, most seems in order, however the below are some points that require your attention 👇 :

• In your affiliations please spell out USA as United States or United States of America.
• github should read Github
• Our guidelines state The paper should be between 250-1000 words. At ~5000 words, the paper is therefore currently too long. I suggest you remove the Methods and Demonstration sections fully and instead incorporate (if you haven't already) such material in your project documentation.

[twj8CDC]

@Kevin-Mattheus-Moerman is there anyway to make an exception on the word limit? I was asked by the reviewers to extend the content to the length the paper is now. Feels like a waste of effort to drop these sections at this point.

[rich2355]

Hi @twj8CDC, so sorry for this, I was not notified or aware of the word limit. As suggested by the AEiC, it would be great to move these 2 sections to a separate link with your documentation. Moving these sections out of paper does not mean throwing them away, people will still be interested in your method and demonstration and will refer to your documentation.

[Kevin-Mattheus-Moerman]

@twj8CDC as @rich2355 also points out, moving the information developed to the documentation means it is not lost. So please process this move to bring the paper closer to our suggested 1000 maximum. Thanks.

[twj8CDC]

@rich2355 @Kevin-Mattheus-Moerman, No worries, just thought I would ask.

I will work on this change. Thanks!