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[REVIEW]: Probabilistic Biostatistics with Julia #36

Closed whedon closed 3 years ago

whedon commented 4 years ago

Submitting author: !--author-handle-->@tszanalytics<!--end-author-handle-- (Jeffrey A Mills) Repository: https://github.com/tszanalytics/Juliacon2019 Branch with paper.md (empty if default branch): Version: Editor: !--editor-->@matbesancon<!--end-editor-- Reviewers: @bkamins, @kescobo Archive: Pending

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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

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

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

The reviewer guidelines are available here: https://proceedings.juliacon.org/guide/reviewers. Any questions/concerns please let @matbesancon know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @bkamins

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

Review checklist for @kescobo

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Paper format

Content

whedon commented 4 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @bkamins, @kescobo it looks like you're currently assigned to review this paper :tada:.

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whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tszanalytics commented 4 years ago

Just an update: I am putting together example code to generate all the figures and the table in the paper. I will post this on the repo soon. I've add a license. I have added a table and made some other changes to the paper, and I am still working on editing the paper - I will upload a revised version soon. I will also add the conference presentation and any related code to the repo once I have that together.

bkamins commented 4 years ago

Thank you for all this. So probably it is best if we wait for the update before reviewing. Right? Please let us know when you are done. Thank you.

Some minor points while you update the text are (this is based on just skimming over the paper - I will read it in derail after the final version is uploaded):

tszanalytics commented 4 years ago

Yes, waiting for the update before reviewing makes sense. I will incorporate all your suggestions above, thanks for these!

kescobo commented 4 years ago

Alright - I'm back. Looks like a lot has happened, but we're waiting on some updates before moving forward with review. Is that right?

tszanalytics commented 4 years ago

Yep, working on my presentation right now! Will update this after the presentation.

bkamins commented 4 years ago

Some small code review comments:

(I can check it if we have reproducible codes)

tszanalytics commented 4 years ago

Thanks Bogumil! I had spotted the wt_draws error but not the Real. Also, thanks for answering Stefan K's question more clearly than I did at my presentation - I chatted with him later and he said you had explained it to him.

At the airport in Baltimore waiting for my flight right now. Wish I could have stayed for the hackathon. Was a fantastic conference. Hope to chat with you at JuliaCon 2020!

bkamins commented 4 years ago

@tszanalytics - thank you for a very nice presentation (and I did not think that you knew that it was me who made the remark - but it turns out you did 😄).

I am obsessed with the difference in interpretation of hypothesis test results in frequentist and Bayesian inference (and actually I think that Bayesian interpretation is more intuitive for most people) and your work fits perfectly into this picture.

tszanalytics commented 4 years ago

@bkamins - Actually I didn't know it was you at the time, I only found out when I chatted with Stefan later. I wish I had known so I could have chatted with you. We must get together at the next time. My flight delayed so more time to work on the proceedings revisions 😄

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tszanalytics commented 4 years ago

@bkamins Ok, recompiled the pdf here. Thanks for pointing me in the right direction.

bkamins commented 4 years ago

@tszanalytics

I think your work is an interesting case study. Here are my comments to your submission (please treat them as suggestions and decide what you think should be incorporated).

Formal requirements of the review process (boxes checked-off above)

Code related

Paper related

A major comment is to give more discussion of your BayesTesting.jl package (design goals, functionality etc. - see questions for reviewers to see what kind of information is expected). Of course please try to keep in the page limit of the proceedings when doing this (this is a soft suggestion).

bkamins commented 4 years ago
matbesancon commented 4 years ago

@tszanalytics did you finish the corrections from @bkamins ?

kescobo commented 4 years ago

I'm a bit confused about whether I'm supposed to be evaluating just the code in the Proceedings repo, BayesTesting.jl or both. This review assumes both, please let me know if I'm mistaken.

Overall

This manuscript presents a justification for and examples of using Bayesian inference in biomedical research, specifically outlining a method using julia to generate "Bayesian p-values" as a bridge from the current frequentist methods typically employed in biological contexts. As a biologist that's just starting to learn about Bayesian methods, I'm excited to have this resource and to have a force in the julia community pushing towards more robust statistical methods.

The manuscript could benefit from some minor updates to present a consistent voice and to provide additional explanation / context in the form of citations for a number of claims. The accompanying code should have substantially more documentation / clarity, both in terms of content and presentation. That said, this effort is definitely worth publishing with some modification.

Manuscript

Comments on the manuscript can be found here: 10.21105.jcon.00036_KSB_comments.pdf

Code

I largely agree with @bkamins ' comments here regarding the need for additional documentation (in a perfect world, there would be runable jupyter notebooks, or you could use something like Literate.jl) and tests.

Other Minor Comments

matbesancon commented 4 years ago

Indeed that's both, thanks

On Wed, Aug 21, 2019, 00:46 Kevin Bonham notifications@github.com wrote:

I'm a bit confused about whether I'm supposed to be evaluating just the code in the Proceedings repo, BayesTesting.jl or both. This review assumes both, please let me know if I'm mistaken. Overall

This manuscript presents a justification for and examples of using Bayesian inference in biomedical research, specifically outlining a method using julia to generate "Bayesian p-values" as a bridge from the current frequentist methods typically employed in biological contexts. As a biologist that's just starting to learn about Bayesian methods, I'm excited to have this resource and to have a force in the julia community pushing towards more robust statistical methods.

The manuscript could benefit from some minor updates to present a consistent voice and to provide additional explanation / context in the form of citations for a number of claims. The accompanying code should have substantially more documentation / clarity, both in terms of content and presentation. That said, this effort is definitely worth publishing with some modification. Manuscript

Comments on the manuscript can be found here: 10.21105.jcon.00036_KSB_comments.pdf https://github.com/JuliaCon/proceedings-review/files/3522868/10.21105.jcon.00036_KSB_comments.pdf Code

I largely agree with @bkamins https://github.com/bkamins ' comments here regarding the need for additional documentation (in a perfect world, there would be runable jupyter notebooks, or you could use something like Literate.jl) and tests. Other Minor Comments

  • There's a "Third Author" in the authors list. I'm guessing that's part of the template slipping through?
  • tszanalytics/BayesTesting.jl#11 https://github.com/tszanalytics/BayesTesting.jl/issues/11
  • Is the raw data for the analyses you perform in the paper accessible? Would be great to have a DataDeps annotation for it so it's easily acquirable to reproduce your analyses.

— You are receiving this because you were assigned. Reply to this email directly, view it on GitHub https://github.com/JuliaCon/proceedings-review/issues/36?email_source=notifications&email_token=AB2FDMRSMWRC57T27UWC5EDQFRX35A5CNFSM4IDVDKJ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4X4ITI#issuecomment-523224141, or mute the thread https://github.com/notifications/unsubscribe-auth/AB2FDMRWLRO7ELAPKC4O53TQFRX35ANCNFSM4IDVDKJQ .

tszanalytics commented 4 years ago

Thanks for the comments all. I have been a bit busy the last week or so, but now this is top of my list. I will get to work revising the paper and the code, etc. to address the comments. Adding a jupyter notebook sounds like a good idea also, so I will have a go at putting one together.

tszanalytics commented 4 years ago

I've just got back to working on this and realized there is some confusion about what is being reviewed. The presentation and the proceedings submission for JuliaCon 2019 was not about the package BayesTesting.jl - I gave a presentation about that in 2018 - so I don't believe that is part of the work currently under review. However, I would be happy to receive any comments and suggestions with regard to the package. I haven't had time to work on developing it further in some time, but hope to do so soon and plan on registering it very soon.

matbesancon commented 4 years ago

ping @tszanalytics, did you have time to work on the corrections?

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

PDF failed to compile for issue #36 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation Berry2017' on page 1 undefined on input line 33 CitationBerry20ll' on page 1 undefined on input line 30 Citation Mills2018' on page 1 undefined on input line 24 CitationMills2018' on page 2 undefined on input line 73 Citation Mills2019' on page 1 undefined on input line 22 CitationMills2019' on page 1 undefined on input line 24 Citation Mills2019' on page 2 undefined on input line 73 CitationMills2019' on page 2 undefined on input line 76 Citation Mills2019' on page 2 undefined on input line 78 CitationRamos2010' on page 2 undefined on input line 58 Citation Strawn2017' on page 1 undefined on input line 24 CitationStrawn2018' on page 1 undefined on input line 24 Citation Strawn2018' on page 2 undefined on input line 78 CitationStrawn2018a' on page 1 undefined on input line 24 Citation Strawn2019' on page 1 undefined on input line 24 CitationWass2019' on page 1 undefined on input line 33 Citation bezanson2017julia' on page 1 undefined on input line 20 Referenceeq:hoh1' on page 2 undefined on input line 60 Reference eq:hoh1' on page 2 undefined on input line 82 Referenceeq:odds' on page 2 undefined on input line 82 Reference eq:pval' on page 2 undefined on input line 82 Referencefig:pars_diff' on page 2 undefined on input line 82 Latexmk: Summary of warnings: Latex failed to resolve 5 reference(s) Latex failed to resolve 19 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.aux'

Run number 2 of rule 'pdflatex'

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation Berry2017' on page 1 undefined on input line 33 CitationBerry20ll' on page 1 undefined on input line 30 Citation Mills2018' on page 1 undefined on input line 24 CitationMills2018' on page 2 undefined on input line 73 Citation Mills2019' on page 1 undefined on input line 22 CitationMills2019' on page 1 undefined on input line 24 Citation Mills2019' on page 2 undefined on input line 73 CitationMills2019' on page 2 undefined on input line 76 Citation Mills2019' on page 2 undefined on input line 78 CitationRamos2010' on page 2 undefined on input line 58 Citation Strawn2017' on page 1 undefined on input line 24 CitationStrawn2018' on page 1 undefined on input line 24 Citation Strawn2018' on page 2 undefined on input line 78 CitationStrawn2018a' on page 1 undefined on input line 24 Citation Strawn2019' on page 1 undefined on input line 24 CitationWass2019' on page 1 undefined on input line 33 Citation bezanson2017julia' on page 1 undefined on input line 20 Referenceeq:odds' on page 2 undefined on input line 82 Reference eq:pval' on page 2 undefined on input line 82 Referencefig:pars_diff' on page 2 undefined on input line 82 Latexmk: Summary of warnings: Latex failed to resolve 3 reference(s) Latex failed to resolve 19 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.out'

Run number 3 of rule 'pdflatex'

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation Berry2017' on page 1 undefined on input line 33 CitationBerry20ll' on page 1 undefined on input line 30 Citation Mills2018' on page 1 undefined on input line 24 CitationMills2018' on page 2 undefined on input line 73 Citation Mills2019' on page 1 undefined on input line 22 CitationMills2019' on page 1 undefined on input line 24 Citation Mills2019' on page 2 undefined on input line 73 CitationMills2019' on page 2 undefined on input line 76 Citation Mills2019' on page 2 undefined on input line 78 CitationRamos2010' on page 2 undefined on input line 58 Citation Strawn2017' on page 1 undefined on input line 24 CitationStrawn2018' on page 1 undefined on input line 24 Citation Strawn2018' on page 2 undefined on input line 78 CitationStrawn2018a' on page 1 undefined on input line 24 Citation Strawn2019' on page 1 undefined on input line 24 CitationWass2019' on page 1 undefined on input line 33 Citation bezanson2017julia' on page 1 undefined on input line 20 Referenceeq:odds' on page 2 undefined on input line 82 Reference eq:pval' on page 2 undefined on input line 82 Referencefig:pars_diff' on page 2 undefined on input line 82 Latexmk: Summary of warnings: Latex failed to resolve 3 reference(s) Latex failed to resolve 19 citation(s) Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

PDF failed to compile for issue #36 with the following error:

rm: cannot remove '*.aux': No such file or directory Latexmk: This is Latexmk, John Collins, 17 Jan. 2018, version: 4.55. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex'

Run number 1 of rule 'pdflatex'

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation Berry2017' on page 1 undefined on input line 33 CitationBerry20ll' on page 1 undefined on input line 30 Citation Mills2018' on page 1 undefined on input line 24 CitationMills2018' on page 2 undefined on input line 73 Citation Mills2019' on page 1 undefined on input line 22 CitationMills2019' on page 1 undefined on input line 24 Citation Mills2019' on page 2 undefined on input line 73 CitationMills2019' on page 2 undefined on input line 76 Citation Mills2019' on page 2 undefined on input line 78 CitationRamos2010' on page 2 undefined on input line 58 Citation Strawn2017' on page 1 undefined on input line 24 CitationStrawn2018' on page 1 undefined on input line 24 Citation Strawn2018' on page 2 undefined on input line 78 CitationStrawn2018a' on page 1 undefined on input line 24 Citation Strawn2019' on page 1 undefined on input line 24 CitationWass2019' on page 1 undefined on input line 33 Citation bezanson2017julia' on page 1 undefined on input line 20 Referenceeq:hoh1' on page 2 undefined on input line 60 Reference eq:hoh1' on page 2 undefined on input line 82 Referenceeq:odds' on page 2 undefined on input line 82 Reference eq:pval' on page 2 undefined on input line 82 Referencefig:pars_diff' on page 2 undefined on input line 82 Latexmk: Summary of warnings: Latex failed to resolve 5 reference(s) Latex failed to resolve 19 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.aux'

Run number 2 of rule 'pdflatex'

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation Berry2017' on page 1 undefined on input line 33 CitationBerry20ll' on page 1 undefined on input line 30 Citation Mills2018' on page 1 undefined on input line 24 CitationMills2018' on page 2 undefined on input line 73 Citation Mills2019' on page 1 undefined on input line 22 CitationMills2019' on page 1 undefined on input line 24 Citation Mills2019' on page 2 undefined on input line 73 CitationMills2019' on page 2 undefined on input line 76 Citation Mills2019' on page 2 undefined on input line 78 CitationRamos2010' on page 2 undefined on input line 58 Citation Strawn2017' on page 1 undefined on input line 24 CitationStrawn2018' on page 1 undefined on input line 24 Citation Strawn2018' on page 2 undefined on input line 78 CitationStrawn2018a' on page 1 undefined on input line 24 Citation Strawn2019' on page 1 undefined on input line 24 CitationWass2019' on page 1 undefined on input line 33 Citation bezanson2017julia' on page 1 undefined on input line 20 Referenceeq:odds' on page 2 undefined on input line 82 Reference eq:pval' on page 2 undefined on input line 82 Referencefig:pars_diff' on page 2 undefined on input line 82 Latexmk: Summary of warnings: Latex failed to resolve 3 reference(s) Latex failed to resolve 19 citation(s) Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'paper.out'

Run number 3 of rule 'pdflatex'

Running 'pdflatex -recorder "paper.tex"'

Latexmk: List of undefined refs and citations: Citation Berry2017' on page 1 undefined on input line 33 CitationBerry20ll' on page 1 undefined on input line 30 Citation Mills2018' on page 1 undefined on input line 24 CitationMills2018' on page 2 undefined on input line 73 Citation Mills2019' on page 1 undefined on input line 22 CitationMills2019' on page 1 undefined on input line 24 Citation Mills2019' on page 2 undefined on input line 73 CitationMills2019' on page 2 undefined on input line 76 Citation Mills2019' on page 2 undefined on input line 78 CitationRamos2010' on page 2 undefined on input line 58 Citation Strawn2017' on page 1 undefined on input line 24 CitationStrawn2018' on page 1 undefined on input line 24 Citation Strawn2018' on page 2 undefined on input line 78 CitationStrawn2018a' on page 1 undefined on input line 24 Citation Strawn2019' on page 1 undefined on input line 24 CitationWass2019' on page 1 undefined on input line 33 Citation bezanson2017julia' on page 1 undefined on input line 20 Referenceeq:odds' on page 2 undefined on input line 82 Reference eq:pval' on page 2 undefined on input line 82 Referencefig:pars_diff' on page 2 undefined on input line 82 Latexmk: Summary of warnings: Latex failed to resolve 3 reference(s) Latex failed to resolve 19 citation(s) Failure to make 'paper.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 1 Refer to 'paper.log' for details Looks like we failed to compile the PDF

tszanalytics commented 4 years ago

@matbesancon Not sure what is going on now. The pdf file looks good when I compile it with TeXstudio, but things are moved around when I compile it here. Now it won't compile at all. Somebody strangle whedon for me.

I've updated the .jl files, added two jupyter notebooks, and substantially revised the paper in light of the comments (thanks everyone for all the great suggestions, etc.). I'll will post a more detailed response once whedon decides to generate the pdf!

matbesancon commented 4 years ago

try compiling locally using latexmk, which is what is used on the server

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tszanalytics commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago 
Attempting PDF compilation. Reticulating splines etc...
whedon commented 4 years ago

:point_right: Check article proof :page_facing_up: :point_left:

tszanalytics commented 4 years ago

@matbesancon @bkamins @kescobo

Thanks everyone for all the great comments and suggestions. I think the paper is greatly improved as a result. I believe everything on the github repo is now up to date and all the changes are incorporated there. Here's a summary of many of the revisions in response to the reviewer suggestions:

• Changed title. • Added email addresses. • Put citations before periods and commas. • Fixed typos in equations (3) and (4) and added cite to Gelman (2004). • Tried changing from Real to Float64, but for this model it turns out it has to be Real because of use of auto-differentation. • Reworded 1st sentence in intro. to make it clearer. • Reworded 3rd paragraph so it makes more sense and to remove “clean code”. • Provided a citation to support the “iron law” and “institutional inertia” statements. • Provided a citation for the Behrens-Fisher problem. • Edited references section to correct several typos, etc. • Fixed typos in the figures. • Increased the font size for the figures to the extent possible (I found this to be particularly difficult!). • Reduced the size of Fig. 3 by only including two sets of time plot + density plot, and explained its purpose further. This allowed the addition of a new figure (Fig. 5) that provides an example of posterior density plots for treatment, placebo and difference. • Reduced the length of the paper so that it fits on 5 pages.

Please let me know if I've missed anything and I will endeavor to fix it.

Thanks, Jeff

kescobo commented 4 years ago

Thanks for edits - I'll take a look first thing next week.

kescobo commented 4 years ago

@tszanalytics Thanks for the edits. I am largely satisfied with the changes. There are just a few outstanding questions/concerns.

  1. I missed this on my first go-through, but it seems like the citation numbers are out of order (eg. Citation 3 comes first, followed by citation 8 etc). I haven't used latex that much, but I thought that citations were put in order automatically. Is something interfering with that? If this is not expected/accepted behavior, I think the citations should be in order.
  2. @matbesancon suggested that we should be evaluating both BayesTesting.jl and the content of the manuscript, but @tszanalytics says otherwise. Can we get clarification on that? I haven't thoroughly evaluated the package, and it should be made clear whether that's part of the review process.
  3. I am happy to see the notebooks included for analysis. Can you please provide a Project.toml and Manifest.toml for (just one that includes all the packages necessary for both should be fine). This will be useful for future readers so they can get the exact versions of the packages you use. Also would be good to include the julia version number you're using I think.
matbesancon commented 4 years ago

For the second point, if the manuscript is about and uses BayesTesting.jl, it should be reviewed with it. Otherwise if the software is contained in the repo of the paper, it should be as suggested versioned & documented

tszanalytics commented 4 years ago

  1. I'm not sure about the citations. It appears to put them in alphabetical order by first author name. I am using \bibliographystyle{juliacon} \bibliography{ref} as the bibliography style as per instructions, so that must be what is wanted for the proceedings?

  2. My presentation and this paper is not about the package and only uses the package somewhat tangentially. I presented a preliminary version of the package at JuliaCon 2018, and plan on updating and registering it to provide a more complete package by next year, so I don't think the package itself is ready for evaluation. The paper and presentation is about application of Julia to analysis of RCTs and meta analysis.

  3. Unfortunately I must admit that I don't really understand toml files and their usage as yet. I will have to read up on this. I believe I would have to specify a particular project to enable generation of toml files that contain only the packages for that project? I'm not sure how to do this yet.
    I included the Julia version and computer specifics in the paper on page 3 (at end of right column).

Thanks!

bkamins commented 4 years ago

Ad. 3 - this is very easy:

  1. start a terminal in the directory of your project and run a Julia session
  2. switch to package manager mode
  3. write activate .
  4. wtire add WHATEVER_PACKAGES_YOU_REQUIRE_FOR_THE_CODES_TO_WORK
  5. exit Julia

In the directory of your project you will have the files @kescobo mentions.