[REVIEW]: CVtreeMLE: Efficient Estimation of Mixed Exposures using Data Adaptive Decision Trees and Cross-Validated Targeted Maximum Likelihood Estimation in R

whedon commented 2 years ago

Submitting author: !--author-handle-->@blind-contours@osorensen<!--end-editor-- Reviewers: @GaryBAYLOR, @cpalmer718, @wleoncio Archive: 10.5281/zenodo.7651354

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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

@GaryBAYLOR & @cpalmer718, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @osorensen 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 ✨

Review checklist for @GaryBAYLOR

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

Conflict of interest

[x] 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

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@blind-contours) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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

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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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 and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

Review checklist for @cpalmer718

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Contribution and authorship: Has the submitting author (@blind-contours) 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

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 and who the target audience is?
[ ] 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?

osorensen commented 1 year ago

@editorialbot set 10.5281/zenodo.7651354 as archive

editorialbot commented 1 year ago

Done! Archive is now 10.5281/zenodo.7651354

osorensen commented 1 year ago

@editorialbot set v1.0 as version

editorialbot commented 1 year ago

Done! version is now v1.0

osorensen commented 1 year ago

@cpalmer718 and @GaryBAYLOR, I want to thank both of you for your incredibly useful and thorough reviews, which have helped improve this submission a lot. Also thanks for your patience in the process.

Thanks to @wleoncio for coming in and give an additional review, which makes sure that this submission now has really good quality.

osorensen commented 1 year ago

@editorialbot recommend-accept

editorialbot commented 1 year ago

Attempting dry run of processing paper acceptance...

editorialbot commented 1 year ago

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

OK DOIs

- 10.1289/ehp.1206187 is OK
- 10.1016/j.envpol.2022.119356 is OK
- 10.1093/biostatistics/kxu058 is OK
- 10.1073/pnas.1510489113 is OK
- 10.1515/ijb-2015-0013 is OK
- 10.2202/1557-4679.1217 is OK
- 10.1111/j.1541-0420.2011.01685.x is OK
- 10.1002/sim.5907 is OK
- 10.1007/978-3-319-65304-4_14 is OK
- 10.1007/978-1-4419-9782-1 is OK
- 10.1007/978-3-319-65304-4 is OK
- 10.2202/1557-4679.1356 is OK
- 10.1111/rssb.12362 is OK
- 10.1111/biom.13375 is OK
- 10.21105/joss.02526 is OK
- 10.5281/zenodo.1342293 is OK
- 10.5281/zenodo.3558313 is OK
- 10.5281/zenodo.3698329 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 1 year ago

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

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/3977, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

GaryBAYLOR commented 1 year ago

@osorensen I'm glad to see the paper is now accepted, and it's my pleasure to participate in the review process! Congratulations! @blind-contours

blind-contours commented 1 year ago

@wleoncio, @cpalmer718 , @GaryBAYLOR , @osorensen - thank you all for the time you have spent reviewing and improving this package. This is my first piece of software that operationalizes a statistical method I created and I have just learned so much! Really appreciate the support.

Kevin-Mattheus-Moerman commented 1 year ago

@blind-contours I am the AEiC for this track and here to help process the last steps. I've checked the archive and paper and have some minor comments that need your attention:

On the archive:

[x] The version tag on your repository is called v1.0-joss, while here and on ZENODO it is listed as v1.0. These need to match. Please check if you can either: rename the release on GitHub to match v1.0 OR update the version here (I can do this) and on ZENODO to match v1.0-joss.
[x] The ZENODO listed license (currently listed as Creative Commons Attribution 4.0 International) should match the software license which is the MIT license.

On the paper:

[x] Check/fix heterogenous -> heterogeneous
[x] Please extend your affiliation with the state and country, and spell out the country in full, e.g. United States of America.

blind-contours commented 1 year ago

Hi @Kevin-Mattheus-Moerman, I've changed the version on ZENODO to v1.0-joss and changed the license to MIT. I've also made and pushed the fix for heterogeneous in the paper and updated the affiliations. Let me know if you need anything else.

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot set v1.0-joss as version

editorialbot commented 1 year ago

Done! version is now v1.0-joss

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot generate pdf

editorialbot commented 1 year ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

Kevin-Mattheus-Moerman commented 1 year ago

@editorialbot accept

editorialbot commented 1 year ago

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

editorialbot commented 1 year ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

editorialbot commented 1 year ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 1 year ago

🚨🚨🚨 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 :point_right: https://github.com/openjournals/joss-papers/pull/3995
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.04181
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

Kevin-Mattheus-Moerman commented 1 year ago

Congratulations on this publication @blind-contours !

Thanks for editing @osorensen!

And a special thanks to the reviewers: @GaryBAYLOR, @cpalmer718, @wleoncio !

editorialbot commented 1 year ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.04181/status.svg)](https://doi.org/10.21105/joss.04181)

HTML:
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  <img src="https://joss.theoj.org/papers/10.21105/joss.04181/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.04181/status.svg
   :target: https://doi.org/10.21105/joss.04181

This is how it will look in your documentation:

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