[REVIEW]: survxai: an R package for model agnostic explanations of survival models #961

whedon · 2018-09-17T20:20:16Z

Submitting author: @AleksandraDabrowska (Aleksandra Grudziąż)
Repository: https://github.com/MI2DataLab/survxai
Version: 0.2.0
Editor: @yochannah
Reviewer: @hiendn, @dirmeier
Archive: 10.5281/zenodo.1477857

Status

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Reviewer instructions & questions

@hiendn & @dirmeier, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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Review checklist for @hiendn

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

Code of Conduct

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General checks

Repository: Is the source code for this software available at the repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: Does the release version given match the GitHub release (0.2.0)?
Authorship: Has the submitting author (@AleksandraDabrowska) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @dirmeier

Conflict of interest

As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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 repository url?
License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
Version: Does the release version given match the GitHub release (0.2.0)?
Authorship: Has the submitting author (@AleksandraDabrowska) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

Authors: Does the paper.md file include a list of authors with their affiliations?
A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

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

whedon · 2018-09-17T20:20:19Z

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @hiendn, it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

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whedon · 2018-09-17T20:20:20Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-09-17T20:21:07Z

👉 Check article proof 📄 👈

hiendn · 2018-09-20T12:18:39Z

Hi @AleksandraDabrowska, I am one of your reviewers! My comments and suggestions will be posted on the issues page of your repository.

yochannah · 2018-10-08T20:39:17Z

Quick status check - looking at the original repo, issues 18 to 21 need to be addressed before we can take this one forward, right?

dirmeier · 2018-10-08T20:47:30Z

Yeah, exactly. From my side these two and 20. All of them are minor changes.

hiendn · 2018-10-08T23:31:03Z

@yochannah that's correct, resolving 22 would be good as well, if possible.

yochannah · 2018-10-21T19:21:28Z

👋 @AleksandraDabrowska - any progress or ETA for the ticket revisions?

dirmeier · 2018-10-26T23:18:43Z

Hey @AleksandraDabrowska - could you rebuild the pdf once you are finished with the reviews? Then I can close the respective issues in your repository.

AleksandraDabrowska · 2018-10-30T09:58:01Z

@whedon generate pdf

whedon · 2018-10-30T09:58:04Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-10-30T09:58:42Z

👉 Check article proof 📄 👈

AleksandraDabrowska · 2018-10-30T14:55:31Z

@whedon generate pdf

whedon · 2018-10-30T14:55:35Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-10-30T14:56:19Z

👉 Check article proof 📄 👈

hiendn · 2018-11-02T01:05:08Z

I am now entirely happy with the with article.

dirmeier · 2018-11-02T19:51:51Z

Likewise. A very nice package, too! :)

AleksandraDabrowska · 2018-11-03T03:02:06Z

@hiendn @dirmeier Thank you very much for reviewing and for your kind words! :)
Should we now issue a DOI for our archive, as it is written in "The review process" section (https://joss.readthedocs.io/en/latest/submitting.html?fbclid=IwAR04SV6oxRM9B3mPL8NXhMhzToU_c3PwwcuiATwttKWaty2rEm8X8aZ19TM)?

yochannah · 2018-11-04T16:17:08Z

@AleksandraDabrowska Looking good! Before generating the archive, though, there is one issue with the manuscript I'd like to fix. Figures 3 and 4 are interspersed with the references in the most recent proof, but I'm reasonably sure they should be up in the main paper text. Can you fix this? Once this is fixed, please do generate an archive and share the URL in this thread!! 🎉

AleksandraDabrowska · 2018-11-05T09:12:56Z

@whedon generate pdf

whedon · 2018-11-05T09:12:59Z

Attempting PDF compilation. Reticulating splines etc...

whedon · 2018-11-05T09:13:28Z

👉 Check article proof 📄 👈

AleksandraDabrowska · 2018-11-05T11:47:30Z

@yochannah here is archive https://zenodo.org/record/1477857#.W-AtQiDdg2w

yochannah · 2018-11-05T22:38:25Z

The figures look better! Thanks @AleksandraDabrowska

yochannah · 2018-11-05T22:40:03Z

@whedon set http://doi.org/10.5281/zenodo.1477857 as archive

whedon · 2018-11-05T22:40:07Z

OK. 10.5281/zenodo.1477857 is the archive.

yochannah · 2018-11-05T22:42:18Z

@arfon I think we're ready to accept this one!

arfon · 2018-11-06T06:35:39Z

@whedon accept

whedon · 2018-11-06T06:35:42Z

Attempting dry run of processing paper acceptance...

whedon · 2018-11-06T06:36:15Z

Check final proof 👉 openjournals/joss-papers#48

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#48, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon · 2018-11-06T06:37:16Z

@whedon accept deposit=true

whedon · 2018-11-06T06:37:19Z

Doing it live! Attempting automated processing of paper acceptance...

whedon · 2018-11-06T06:38:01Z

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.00961 joss-papers#49
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00961
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

arfon · 2018-11-06T07:06:16Z

@hiendn, @dirmeier - many thanks for your reviews here, and to @yochannah for editing this submission ✨

@AleksandraDabrowska - your paper is now accepted into JOSS ⚡ 🚀 💥

whedon · 2018-11-06T07:06:18Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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whedon assigned yochannah Sep 17, 2018

whedon added the review label Sep 17, 2018

whedon mentioned this issue Sep 17, 2018

[PRE REVIEW]: survxai: an R package for model agnostic explanations of survival models #929

Closed

This was referenced Oct 30, 2018

Corrections to JOSS manuscript MI2DataLab/survxai#18

Closed

Failure to install from the GitHub repo MI2DataLab/survxai#22

Closed

yochannah added the accepted label Nov 5, 2018

arfon closed this as completed Nov 6, 2018

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[REVIEW]: survxai: an R package for model agnostic explanations of survival models #961

[REVIEW]: survxai: an R package for model agnostic explanations of survival models #961

Comments

whedon commented Sep 17, 2018 • edited Loading

Status

Reviewer instructions & questions

Review checklist for @hiendn

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @dirmeier

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented Sep 17, 2018

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whedon commented Sep 17, 2018

hiendn commented Sep 20, 2018

yochannah commented Oct 8, 2018 • edited Loading

dirmeier commented Oct 8, 2018

hiendn commented Oct 8, 2018

yochannah commented Oct 21, 2018

dirmeier commented Oct 26, 2018

AleksandraDabrowska commented Oct 30, 2018

whedon commented Oct 30, 2018

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AleksandraDabrowska commented Oct 30, 2018

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AleksandraDabrowska commented Nov 3, 2018

yochannah commented Nov 4, 2018

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yochannah commented Nov 5, 2018

arfon commented Nov 6, 2018

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