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[REVIEW]: bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework #1541
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @paul-buerkner, @tjmahr it looks like you're currently assigned to review 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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I have just finished my review and have very few minor comments.
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Thank you for the thorough review, @paul-buerkner! |
Dear @paul-buerkner, thanks a lot for your comments! We addressed them in this PR:
Please note that there are still some references for which we did not find a DOI: we continue our search in the meantime. We hope you will find the revised version satisfying |
Looks good to me. |
@tjmahr, are you still able to review this submission? @paul-buerkner, thanks again!! |
I would like to review it but won't be able to look at it until next week. |
@tjmahr, no problem, thanks for following up! |
@whedon generate pdf |
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Please take me off of the list of reviewers. I have received over a dozen e-mails on four projects today.
The first project, yesterday, generated ~30 e-mails to me, most of them not understandable.IMHO, your process for reviewing needs serious work.
Sincerely,
Barry
On Thursday, July 25, 2019, 6:38:25 AM EDT, whedon <[email protected]> wrote:
👉 Check article proof 📄 👈
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@BarryDeCicco, you should unsubscribe from the GitHub notifications for this repository, or otherwise change your notification settings. See the second post (#1541 (comment)) in this review thread (same information is available in every review thread). |
I worked with version 0.2.4, the most recent on the GitHub repository, although the version mentioned in the checklist is 0.2.3
I do not see anything for contribution guidelines. I would add a CommentsThe amount of documentation to support the package is very generous. For my review, however, I focused on the README and the software paper. This package borrows a lot from the Kruschke school of Bayesian inference. HDI and ROPE are a distinct feature of his tutorials and textbook; one does not see them very often in works by, say, Stan developers. Therefore, this package is tremendously useful for those reading his tutorials, or for people like me, who occasionally will quantify an effect with a ROPE percentage or who want to learn about using Bayes factors. The ROPE procedure and other indices use the highest density interval. Is there any option to use an equal-tailed interval? READMEI was confused by the README. When I see R code followed immediately by a plot, I assume that the R code produced the plot. But the functions in the README produce text output (which is not included in the README) and they do not produce plots. I would include the text output of the R code. I would also note that the figures there are diagrams meant to illustrate the statistical concept. The software paper does a good job of making this point clear. I don't see a demo for
The primeness of 89 is not important. McElreath's choice of 89 in Statistical Rethinking text was to illustrate that interval widths are arbitrary and that there is nothing special about 95 or 90 compared to 89.
Needs a verb. I don't understand the Bayes Factor diagram in the README.
This range is the same number twice.
Should this have a reference?
I don't see a demo for the area under the curve functions. Documentation
I don't understand how a p-value can get a negative percentage. What would a 0% p-value mean? If this index doesn't act like a familiar p-value, it is probably the wrong name for it. Software paperThe first mention of bayestestR in the second paragraph is awkward. Specifically, the text shifts from talking about common ways to describe effects in a Bayesian framework to talking about the features of the package:
It's great that the output of
I don't see any plotting examples in the README or documentation pages. I see plotting methods in the NAMESPACE. I think it would worthwhile to demonstrate that the functions demoed in the article also work on models. For example, I can call Proofreading concernsEvery reference of Kruschke spells out the author's full name. Figure 2 should be referenced in the text.
Needs a comma.
Allows one.
Nevertheless doesn't make sense.
Based. The system for building the references section should protect some words from being converted to lowercase. (In LaTeX, this is done with {}). Right now, for example, it says |
Dear @tjmahr, thanks a lot for your thorough review. We have addressed them in this PR:
We hope you will be satisfied with the revisions |
@whedon generate pdf |
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Just fix the typo in Savage-Dickey, and I'm satisfied. |
Also, thanks, in particular, for adding the ETI functionality for the ROPE methods. |
👋 @DominiqueMakowski - please see easystats/bayestestR#217 and merge it - also carefully check the rest of the bib to make sure I didn't miss anything else (e.g., words in lower case that should be in upper case, odd periods at the end of titles, etc.) |
@danielskatz Thanks for the thorough reading! I have read the paper and checked all hyperlinks, everything looks good so far. I'll go through the paper and check the references now. |
@whedon generate pdf |
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In addition, here are some changes for the paper. (in a PR that I forgot to add but has now been merged) :) |
Thanks for the language editing! i have gone through the references and found some minor changes. I will hand over to @DominiqueMakowski for the final check. |
Ok - please let me know when you & @DominiqueMakowski are done, then we can proceed. |
@whedon generate pdf |
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@danielskatz Thanks a lot for your changes! |
@whedon accept |
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Check final proof 👉 openjournals/joss-papers#901 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#901, 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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@cMadan @danielskatz @paul-buerkner @tjmahr Thanks a lot again for your time and contributions! 😍 |
👋 @paul-buerkner Might you have the bandwidth to review the following submission? [PRE REVIEW]: jointVIP: Prioritizing variables in observational study design with joint variable importance plot in R |
Hey! I am currently swamped with reviews that I still have to complete so I cannot accept new ones right now unfortunately. |
Submitting author: @DominiqueMakowski (Dominique Makowski)
Repository: https://github.com/easystats/bayestestR
Version: 0.2.5
Editor: @cMadan
Reviewer: @paul-buerkner, @tjmahr
Archive: 10.5281/zenodo.3361605
Status
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@paul-buerkner & @tjmahr, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
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✨ Please try and complete your review in the next two weeks ✨
Review checklist for @paul-buerkner
Conflict of interest
Code of Conduct
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Software paper
paper.md
file include a list of authors with their affiliations?Review checklist for @tjmahr
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
paper.md
file include a list of authors with their affiliations?The text was updated successfully, but these errors were encountered: