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[REVIEW]: hal9001: Scalable highly adaptive lasso regression in R #2526
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @daviddewhurst, @rrrlw it looks like you're currently assigned to review this paper 🎉. Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post. ⭐ 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 check references |
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1 similar comment
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@daviddewhurst, @rrrlw: Thanks for agreeing to review. Please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. If possible create issues (and cross-reference) in the submission's repository to avoid too specific discussions in this review thread. If you have any questions or concerns please let me know. |
@daviddewhurst, please let me or @nhejazi know if there's anything we can do. (This is not meant as a "please hurry", merely as a friendly comment that we are here to help if you need anything.) |
@daviddewhurst, can you please let me know how your review is progressing? |
@mikldk I've been completing it and not updating the above page. It'll be finished on Friday. |
See completed review (except for two bullet point) and corresponding two issues on repo. |
@nhejazi: What is the status of the opened issues related to this review? This is not to rush you, merely to give me an impression of the progress and time-frame. |
Thanks for checking in @mikldk. tlverse/hal9001#71 contains all changes related to the issues brought to my attention. The only outstanding issue afaik is tlverse/hal9001#69, which recommends a few real data analysis examples. I don't have any prepared offhand, so I may ask that this be deferred as something we should add in the future rather than for the JOSS review (any input from @daviddewhurst also welcome on this). I think it's a good suggestion but, in the meantime, we could, e.g., point to data analysis sections of existing academic manuscripts. |
@nhejazi I think it would be a great idea to refer to a few places where HAL is used - both in |
Apologies for the delay with this review - overall, this looks like a solid submission. The (minor) issues that I opened were addressed and closed. I think this will be a useful addition to the JOSS literature. I have left the "Examples" box unchecked until it's addressed (looks like pointing to data analysis sections of existing manuscripts (ideally ones that have the source code available?) in paper.md and in the help pages will work). As such, once the "Examples" box is addressed, I feel comfortable recommending this package + manuscript be accepted to JOSS. I do have an optional suggestion on how the package could be improved - a vignette on using it with tidymodels. Although not everyone subscribes to the tidymodels way of doing things, its use has grown over time and it might be worth adding an example or two showing how tidymodels users could take advantage of hal9001. Other than that, I think this is a solid package, as is evidenced by its use in multiple academic manuscripts. Thank you to the authors for this valuable contribution! |
Thanks @mikldk and @rrrlw, I'll add a few references in an Applications section of the paper draft and add code from one such project that I was involved in. This will cover how to use HAL in constructing a popular inverse probability weighted estimator that is prominent in the causal inference literature. I'll ping here again when that's done so that we can discuss any lingering details to finish up the review. @rrrlw, thanks for noting a possible tidymodels integration. I like this idea and have some plans to modularize hal9001 (in a subsequent major release). If you don't mind opening up an issue about this, I'll keep track of it there and try to make these changes at the same time. |
I've just added an Applications section to the JOSS paper draft (tlverse/hal9001@640e773), which briefly reviews and details the use of HAL regression in four very recent papers. I've tried to go through HAL was used in each paper and point out what advances were made by relying upon the |
@nhejazi sure, that's fine. I'll close the issue. |
@mikldk This does it for me -- my review is complete. |
@whedon generate pdf |
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@daviddewhurst, @rrrlw Thank you very much for your effort in reviewing this paper! |
@whedon accept |
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#1756 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1756, then you can now move forward with accepting the submission by compiling again with the flag
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Hi @mikldk, I can address the missing DOI 10.1111/biom.13375 if necessary (the paper was just accepted this week), but I don't think it would be a problem to accept as is, since the two submissions were ongoing concurrently. Happy to address this if it's an issue. Thanks for your work in curating/editing this JOSS submission. |
@nhejazi If you have an updated DOI then please use that. |
@mikldk Ok, I've fixed the missing DOI identified by whedon and finalized a new Zenodo release for this submission. That Zenodo archive has DOI 10.5281/zenodo.4050561. We should be all set to finalize. |
@whedon check references |
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@whedon generate pdf |
Proof LGTM! I'm not sure I can run whedon accept myself so I'll just wait on that one. |
@whedon set 10.5281/zenodo.4050561 as archive |
OK. 10.5281/zenodo.4050561 is the archive. |
@whedon accept |
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👋 @openjournals/joss-eics, this paper is ready to be accepted and published. Check final proof 👉 openjournals/joss-papers#1757 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1757, then you can now move forward with accepting the submission by compiling again with the flag
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@whedon accept deposit=true |
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦 |
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@daviddewhurst, @rrrlw - many thanks for your reviews here and to @mikldk for editing this submission ✨ @nhejazi - your paper is now accepted into JOSS ⚡🚀💥 |
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Submitting author: @nhejazi (Nima Hejazi)
Repository: https://github.com/tlverse/hal9001
Version: v0.2.7
Editor: @mikldk
Reviewer: @daviddewhurst, @rrrlw
Archive: 10.5281/zenodo.4050561
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