[PRE REVIEW]: Kirstine.jl: A Julia Package for Bayesian Optimal Design of Experiments

[editorialbot]

Submitting author: !--author-handle-->@lsandig<!--end-author-handle-- (Ludger Sandig) Repository: https://github.com/lsandig/Kirstine.jl Branch with paper.md (empty if default branch): paper-draft Version: v0.5.0 Editor: !--editor-->@sneakers-the-rat<!--end-editor-- Reviewers: @harisorgn, @roualdes Managing EiC: Arfon Smith

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Thanks for submitting your paper to JOSS @lsandig. Currently, there isn't a JOSS editor assigned to your paper.

@lsandig if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1085.1 files/s, 196414.4 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
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Markdown                        20           1139              0           4899
Julia                           43            812            737           4703
TeX                              1             10              0            116
TOML                             5              8             10             56
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SUM:                            69           1969            747           9774
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 915

[editorialbot]

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

OK DOIs

- 10.1214/ss/1177009939 is OK
- 10.1201/b15054 is OK
- 10.18637/jss.v095.i13 is OK
- 10.1111/insr.12107 is OK
- 10.1080/01621459.2013.806268 is OK
- 10.1109/icnn.1995.488968 is OK

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A Fresh Approach To Numerical Computing
- 10.1016/s0169-2607(03)00073-7 may be a valid DOI for title: POPED, a Software for Optimal Experiment Design in Population Kinetics
- 10.1016/j.cmpb.2012.05.005 may be a valid DOI for title: PopED: an Extended, Parallelized, Nonlinear Mixed Effects Models Optimal Design Tool

INVALID DOIs

- None

[editorialbot]

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

[editorialbot]

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⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[arfon]

@lsandig - thanks for your submission to JOSS. We're currently managing a large backlog of submissions and the editor most appropriate for your area is already rather busy.

For now, we will need to waitlist this paper and process it as the queue reduces. Thanks for your patience!

[arfon]

@editorialbot invite @sneakers-the-rat as editor

:wave: @sneakers-the-rat – would you be willing to edit this submission for JOSS?

[editorialbot]

Invitation to edit this submission sent!

[sneakers-the-rat]

Yes! I would be willing to edit this, I'll return tomorrow to begin the process :)

@editorialbot assign me as editor

[sneakers-the-rat]

@lsandig I see the main repository is at sourcehut - https://sr.ht/~lsandig/Kirstine.jl/

typically a review will involve raising issues/PRs in the repository, and that serves both as a record of the review and as a way to coordinate work with the authors. I want to respect your choice of git host, but also satisfy the archival needs of JOSS which is currently on github. Do you have preferences or guides for us here - would raising the issues on github be ok for the purposes of review, or is there some way of mirroring them between sourcehut and github?

@arfon is there a way we usually handle this?

[arfon]

@sneakers-the-rat – our only conditions about git hosting are that it's possible for people to open issues/provide feedback, and that there isn't a manual process for account creation (e.g., institutional hosts).

As @lsandig has created a mirror, I think it's OK for the review feedback to be provided on the GitHub mirror (https://github.com/lsandig/Kirstine.jl) but at the end of the review we might want to update the URL of the repository for the paper back to the sourcehut URL (https://sr.ht/~lsandig/Kirstine.jl/).

[arfon]

Yes! I would be willing to edit this, I'll return tomorrow to begin the process :)

@editorialbot assign me as editor

BTW, commands to @editorialbot need to be at the start of a comment @sneakers-the-rat.

[arfon]

@editorialbot assign @sneakers-the-rat as editor

[editorialbot]

Assigned! @sneakers-the-rat is now the editor

[lsandig]

As @lsandig has created a mirror, I think it's OK for the review feedback to be provided on the GitHub mirror (https://github.com/lsandig/Kirstine.jl)

I've now enabled issues on the mirror so you can provide feedback here on github.

but at the end of the review we might want to update the URL of the repository for the paper back to the sourcehut URL (https://sr.ht/~lsandig/Kirstine.jl/).

Yes, it would be great if the link in the final paper could point to the sourcehut repo.

I'm looking forward to your comments!

[lsandig]

MISSING DOIs

- 10.1137/141000671 may be a valid DOI for title: Julia: A Fresh Approach To Numerical Computing
- 10.1016/s0169-2607(03)00073-7 may be a valid DOI for title: POPED, a Software for Optimal Experiment Design in Population Kinetics
- 10.1016/j.cmpb.2012.05.005 may be a valid DOI for title: PopED: an Extended, Parallelized, Nonlinear Mixed Effects Models Optimal Design Tool

I've also verified that these are the correct dois and added them to the bib file.

[sneakers-the-rat]

Fabulous. and it looks like there is at least one way to mirror issues back to sourcehut if you want to keep issues there for your own records. https://github.com/aThorp96/sourcehut_issue_mirror

I'll start searching for reviewers! @lsandig please feel free to recommend any reviewers, here is a list of people who have signed up to review with JOSS: https://reviewers.joss.theoj.org/reviewers

[sneakers-the-rat]

I wonder if @jflournoy , @coryc3133 , or @dcosme (hi!) as experimental design/modeling experts speak julia and would be interested in reviewing this?

Otherwise I see @lbluque and @Dom-Owens-UoB listing themselves as knowing Julia and regressino models.

[jflournoy]

Very intriguing work. I don't speak Julia, though. Not yet.

[Coryc3133]

Sorry, I also don't speak Julia (yet), unfortunately. Sounds like interesting work!

On Tue, Feb 20, 2024, 1:01 PM John Flournoy @.***> wrote:

Very intriguing work. I don't speak Julia, though. Not yet.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6193#issuecomment-1954777984, or unsubscribe https://github.com/notifications/unsubscribe-auth/AEXNC3MZKV3EUYGZCQJOMZ3YUTQIRAVCNFSM6AAAAABBTKJRIKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSNJUG43TOOJYGQ . You are receiving this because you were mentioned.Message ID: @.***>

[sneakers-the-rat]

Thanks yall! Ill keep looking, but appreciate the response. Hope you have been well :)

[harisorgn]

Hello, this seems very interesting, I would be happy to review!

I've never reviewed for JOSS before, so would appreciate any guidance in the process. I'm comfortable in Julia and Bayesian statistics though, so that's something 😅 .

[sneakers-the-rat]

@editorialbot add @harisorgn as reviewer

excellent!!!! I will give you more information once we find a second reviewer and get started, and of course will be available throughout the process for questions. For now the review guides are here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html here: https://joss.readthedocs.io/en/latest/review_criteria.html and here! https://joss.readthedocs.io/en/latest/review_checklist.html

@lsandig do you have any other potential reviewers to recommend?

[editorialbot]

@harisorgn added to the reviewers list!

[harisorgn]

I could ask around the Julia language Slack if that's useful? There are dedicated channels to statistics & Bayesian methods.

[sneakers-the-rat]

That would be lovely if you wouldn't mind :)

[harisorgn]

@roualdes is interested in reviewing as well!

[sneakers-the-rat]

@roualdes can I take that thumb as a confirmation? if so then I believe we can start the review :)

[roualdes]

@sneakers-the-rat yes, confirmed. Happy to review.

[sneakers-the-rat]

@editorialbot add @roualdes as reviewer

wonderful. let's start the review then. that will be on a different issue ( #6424), and i'll see you over there ;)

[editorialbot]

@roualdes added to the reviewers list!

[sneakers-the-rat]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6424.