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Sign up[REVIEW]: bayestestR: Describing Effects and their Uncertainty, Existence and Significance within the Bayesian Framework #1541
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whedon
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cMadan
Jul 2, 2019
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Jul 2, 2019
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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 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
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paul-buerkner
Jul 3, 2019
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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! |
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DominiqueMakowski
commented
Jul 19, 2019
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 |
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Looks good to me. |
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@tjmahr, are you still able to review this submission? @paul-buerkner, thanks again!! |
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I would like to review it but won't be able to look at it until next week. |
whedon
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tjmahr
Jul 23, 2019
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@tjmahr, no problem, thanks for following up! |
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strengejacke
commented
Jul 25, 2019
@whedon generate pdf |
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BarryDeCicco
commented
Jul 25, 2019
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 <notifications@github.com> wrote:
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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). |
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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 |
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DominiqueMakowski
commented
Jul 30, 2019
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 |
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strengejacke
commented
Jul 30, 2019
@whedon generate pdf |
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Just fix the typo in Savage-Dickey, and I'm satisfied. |
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Also, thanks, in particular, for adding the ETI functionality for the ROPE methods. |
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@whedon set 10.5281/zenodo.3361605 as archive |
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OK. 10.5281/zenodo.3361605 is the archive. |
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@DominiqueMakowski, perfect, thank you! @openjournals/joss-eics, I think we're all set to accept here! |
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danielskatz
commented
Aug 12, 2019
@whedon generate pdf |
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danielskatz
commented
Aug 12, 2019
Thanks to @paul-buerkner and @tjmahr for reviewing and @cMadan for editing |
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danielskatz
commented
Aug 12, 2019
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strengejacke
commented
Aug 12, 2019
@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. |
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strengejacke
commented
Aug 12, 2019
@whedon generate pdf |
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danielskatz
commented
Aug 12, 2019
•
In addition, here are some changes for the paper. (in a PR that I forgot to add but has now been merged) :) |
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strengejacke
commented
Aug 12, 2019
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. |
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danielskatz
commented
Aug 12, 2019
Ok - please let me know when you & @DominiqueMakowski are done, then we can proceed. |
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DominiqueMakowski
commented
Aug 13, 2019
@whedon generate pdf |
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DominiqueMakowski
commented
Aug 13, 2019
@danielskatz Thanks a lot for your changes! |
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danielskatz
commented
Aug 13, 2019
@whedon accept |
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Check final proof 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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danielskatz
commented
Aug 13, 2019
@whedon accept deposit=true |
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whedon
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Aug 13, 2019
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Here's what you must now do:
Any issues? notify your editorial technical team... |
danielskatz
closed this
Aug 13, 2019
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If you would like to include a link to your paper from your README use the following code snippets:
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DominiqueMakowski
commented
Aug 13, 2019
@cMadan @danielskatz @paul-buerkner @tjmahr Thanks a lot again for your time and contributions! |
whedon commentedJul 2, 2019
•
edited
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
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paper.md
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Software paper
paper.md
file include a list of authors with their affiliations?