[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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Status

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Markdown: [![status](https://joss.theoj.org/papers/e3f631afd3bbcd60ed5d965ce26a39b0/status.svg)](https://joss.theoj.org/papers/e3f631afd3bbcd60ed5d965ce26a39b0)

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:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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?

lightning-auriga commented 1 year ago

@osorensen I see the markdown file in the repo, which is good, but the links to it in the readme are broken: e.g. should be https://github.com/blind-contours/CVtreeMLE/blob/main/contributing.md but instead is https://github.com/blind-contours/%20CVtreeMLE/blob/main/CONTRIBUTING.md (note floating space). Additionally, the article citation in the markdown readme seems to be malformed.

Regardless, I see the contributing doc, so while the above should be fixed, I'll check the thing off. I'm sorry this has languished.

osorensen commented 1 year ago

Thanks you very much for checking this @cpalmer718, and also for your patience and your thorough review.

@blind-contours, could you please fix the issues mentioned by @cpalmer718.

blind-contours commented 1 year ago

Thanks @cpalmer718 I have fixed the issue with the contributing link and have simply removed the citation for now until we get our paper on Arxiv which should happen soon. I will update the readme with the JOSS citation and Arxiv citation once complete.

osorensen commented 1 year ago

:wave: @tkmamidi, @FrancisXL2019, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The review of this submission has been going on for a while and the authors has addressed a number of issues, but we have lost contact with one of the reviewers. We would hence very much appreciate the opinion of one or two additional reviewers.

osorensen commented 1 year ago

:wave: @yidan-yang @n8thangreen @max-little @skiptoniam, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The review of this submission has been going on for a while and the authors has addressed a number of issues, but we have lost contact with one of the reviewers. We would hence very much appreciate the opinion of one or two additional reviewers.

osorensen commented 1 year ago

@blind-contours, just to let you know, since I'm not getting a response from @GaryBAYLOR, I'm trying to find at least another reviewer for this submission.

osorensen commented 1 year ago

@editorialbot add @wleoncio as reviewer

editorialbot commented 1 year ago

@wleoncio added to the reviewers list!

wleoncio commented 1 year ago

Review checklist for @wleoncio

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 https://github.com/blind-contours/CVtreeMLE?
[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
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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, who the target audience is, and its relation to other work?
[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?

skiptoniam commented 1 year ago

@osorensen I can have a look if you need a second reviewer.

osorensen commented 1 year ago

Perfect, thanks @skiptoniam!

osorensen commented 1 year ago

@editorialbot add @skiptoniam as reviewer

editorialbot commented 1 year ago

@skiptoniam added to the reviewers list!

skiptoniam commented 1 year ago

Review checklist for @skiptoniam

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/blind-contours/CVtreeMLE?
[ ] 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
[ ] 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?

wleoncio commented 1 year ago

Dear @blind-contours,

Thank you for your submission. It successfully checks nearly all points on my checklist, so I see little impediment to giving it a pass. However, there were a few kinks in installation, execution and unit testing that I wish would be dealt with at some point, especially #24:

Looking forward to your reply on those. :)

osorensen commented 1 year ago

Thanks for your review @wleoncio! Looking forward to your response, @blind-contours.

blind-contours commented 1 year ago

@osorensen I've responded to @wleoncio issues and made updates to the package accordingly. There are still some things I can update moving forward to make installation easier but it should be better now.

osorensen commented 1 year ago

Thanks @blind-contours. When you have time, please let us know if this addresses you concerns, @wleoncio.

wleoncio commented 1 year ago

Hi @osorensen,

I think we've made some progress, issues 24 and 25 are taken care of, and 23 and 26 may be left as future improvements.

Regarding 27, however, I'd like to hear back from @blind-contours once more about the possibility of further reducing test times.

wleoncio commented 1 year ago

Dear @osorensen,

Happy to report all my concerns with this submission have been addressed.

osorensen commented 1 year ago

Thanks a lot for your review @wleoncio!

osorensen commented 1 year ago

@wleoncio could you then please also check the missing boxes in your review checklist a bit further up in this thread?

osorensen commented 1 year ago

👋 @skiptoniam could you please update us on how it's going with your review?

blind-contours commented 1 year ago

Is there anything else I can do to help expedite this review process?

osorensen commented 1 year ago

Is there anything else I can do to help expedite this review process?

I'm afraid not, but since we now have two reviewers approving the package, if we don't hear back from @GaryBAYLOR or @skiptoniam within two weeks, I'll move forward with accepting the submission.

GaryBAYLOR commented 1 year ago

Hi @osorensen, thank you for your patience in waiting for my review results. I checked all previous open issues and added a new one today, all of which have now been addressed by the author with the exception of only this one: https://github.com/blind-contours/CVtreeMLE/issues/2. After this is addressed, I am good on my end.

Refer to https://github.com/blind-contours/CVtreeMLE/issues?q=is%3Aissue+is%3Aclosed for all closed issues.

blind-contours commented 1 year ago

I just addressed this issue related to the license: https://github.com/blind-contours/CVtreeMLE/issues/2

GaryBAYLOR commented 1 year ago

@osorensen, all open issues on my end have been addressed.

osorensen commented 1 year ago

Thank you very much @GaryBAYLOR

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot check references

editorialbot commented 1 year ago

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

OK DOIs

- 10.1093/biostatistics/kxu058 is OK
- 10.1097/01.ee9.0000606120.58494.9d 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

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

blind-contours commented 1 year ago

New PDF is compiled and in the package with these edits.

blind-contours commented 1 year ago

The only last thing is getting the package to install on Windows via github actions, I keep getting this error:

cannot open file 'C:\Users\RUNNER~1\AppData\Local\Temp\RtmpoZc4PS\xshell1a402bd4033': Permission denied

I can't find a solution to this - have any of the reviewers seen this Windows error before? I'd just like this to show green checks on all operating systems per reviewers requests.

wleoncio commented 1 year ago

Doesn't ring a bell, but notice how the installation of TinyTeX also doesn't go smoothly.

Perhaps updating your r-lib setup versions (see template here) helps. The new versions may even allow you to remove some manual installation commands from your YAML as well (namely, TinyTeX and the package dependencies).

osorensen 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:

osorensen commented 1 year ago

@editorialbot check references

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
- 10.1097/01.ee9.0000606120.58494.9d 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

osorensen commented 1 year ago

@blind-contours; in the reference list, Keil et al. (2019) is listed as an arXiv preprint, but the doi points me to a paper in Environmental Epidemiology. Could you please correct this reference?

blind-contours commented 1 year ago

Fixed.

osorensen commented 1 year ago

@editorialbot generate pdf

osorensen commented 1 year ago

@editorialbot check references

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

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

osorensen commented 1 year ago

@blind-contours, at this point could you:

[ ] Make a tagged release of your software, and list the version tag of the archived version here.
[ ] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[ ] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[ ] Please list the DOI of the archived version here.

I can then move forward with recommending acceptance of the submission.

osorensen 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:

blind-contours commented 1 year ago

@osorensen

I've created a new release at https://github.com/blind-contours/CVtreeMLE/releases/tag/v1.0-joss

and a Zenodo archive of that release at https://zenodo.org/record/7651354

The DOI for that release is 10.5281/zenodo.7651354

openjournals / joss-reviews