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

[editorialbot]

Submitting author: @lsandig (Ludger Sandig)
Repository: https://git.sr.ht/~lsandig/Kirstine.jl
Branch with paper.md (empty if default branch): joss-paper
Version: v0.6.0
Editor: @sneakers-the-rat
Reviewers: @harisorgn, @roualdes
Archive: 10.5281/zenodo.11185430

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/f6044a0f4e296313f18df2d42a89e1e8"><img src="https://joss.theoj.org/papers/f6044a0f4e296313f18df2d42a89e1e8/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/f6044a0f4e296313f18df2d42a89e1e8/status.svg)](https://joss.theoj.org/papers/f6044a0f4e296313f18df2d42a89e1e8)

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

@harisorgn & @roualdes, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @sneakers-the-rat know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @roualdes

📝 Checklist for @harisorgn

[editorialbot]

Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

For a list of things I can do to help you, just type:

@editorialbot commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@editorialbot generate pdf

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1064.7 files/s, 192765.6 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Markdown                        20           1139              0           4899
Julia                           43            812            737           4703
TeX                              1             10              0            118
TOML                             5              8             10             56
-------------------------------------------------------------------------------
SUM:                            69           1969            747           9776
-------------------------------------------------------------------------------


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

- 10.1137/141000671 is OK
- 10.1214/ss/1177009939 is OK
- 10.1201/b15054 is OK
- 10.1016/s0169-2607(03)00073-7 is OK
- 10.1016/j.cmpb.2012.05.005 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

- None

INVALID DOIs

- None

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[sneakers-the-rat]

OK welcome @harisorgn and @roualdes and thank you for your time here.

As the top issue says, you'll be working from a checklist, a set of guidelines, and some review criteria.

The goal here is to collaboratively help this package reach a basic standard for usability, maintainability, and correctness - we are all friends here, there are no gates to be kept, we're just trying to learn from and help each other out. Feel free to talk amongst each other as peers, this is an open and iterative review, so you don't need to wait until you've reviewed everything before raising an issue or commenting.

The checklist is a set of minimum standards that the package has to meet, but you are also free to read, comment, raise issues and pull requests, and do whatever else falls under your purview as a reviewer. Think about what you would want to have if you were a potential new user of the package - is the documentation clear? do the tests cover what they need to? etc. That kind of neutral third-party perspective is invaluable for making software accessible and maintainable.

As you review, i would suggest that you raise issues in the repository and link back to this issue so that we can track issues related to this review. Since github issues don't have threading, this is how we can keep discussion organized, because commenting in this issue can be a bit messy. Don't be shy commenting here to ask questions about the review itself, though! It's up to you all and the maintainers if you want to follow any sort of naming convention for issues/PRs. This repository is hosted on sourcehut and mirrored to github, but for the purposes of recordkeeping for this review, lets keep the issues on GH and we'll change the repo link to sourcehut at the end.

Time spent reviewing can range from a few hours just completing the checklist to longer depending on how much attention to detail you want to give - I have completed a review in as little as 1 hour when it was obvious everything was shipshape and the authors didn't need any help, and as long as several months when i was helping the authors establish docs and tests. That's up to you! Your time is your gift to give.

Other than that, i'll be here so feel free to ask questions! The first thing you'll want to do is generate your checklists using the commands in the OP comment

[roualdes]

Review checklist for @roualdes

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/lsandig/Kirstine.jl?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@lsandig) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[harisorgn]

Review checklist for @harisorgn

Conflict of interest

• I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

• I confirm that I read and will adhere to the JOSS code of conduct.

General checks

• Repository: Is the source code for this software available at the https://github.com/lsandig/Kirstine.jl?
• License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
• Contribution and authorship: Has the submitting author (@lsandig) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
• Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
• Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
• Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
• Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

• Installation: Does installation proceed as outlined in the documentation?
• Functionality: Have the functional claims of the software been confirmed?
• Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
• Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
• Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
• Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
• Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

• Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
• State of the field: Do the authors describe how this software compares to other commonly-used packages?
• Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[roualdes]

I made it through the draft paper and filed Issue #2 with a few comments.

[roualdes]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[roualdes]

While checking Functionality > Performance, I compared Kirstine.jl to the R package ICAOD, which references the associated paper A Metaheuristic Adaptive Cubature Based Algorithm to Find Bayesian Optimal Designs for Nonlinear Models. In Section 4.2 Sigmoid Emax Model of the linked paper, with code in the supplementary materials, the authors use nearly the same model as in the Getting Started section of Kirstine.jl's doc. The main differences, as far as I could tell, were the priors and the underlying algorithm used to find the optimal design. Here's some comments relative to this experience.

• I could not force the priors in the R code to match the priors in Kirstine.jl's Getting Started example. Instead, I could relative easily make Kisrtine.jl code match the examples in the R code. This is a compliment to the documentation and design of Kirstine.jl
• The R code I ran was just slightly faster than my Julia code. Because the two packages are using different underlying algorithms to find optimal designs, I don't think this conclusion is very meaningful. And I agree with @lsandig's overall statements about Kirstine's design, namely the added ease/flexibility in Kirstine.jl's one language solution to these problems, unlike in R which has to resort to C/C++ for efficient code.

[roualdes]

Issue #3 has some comments/questions related to doc.

[lsandig]

The main differences, as far as I could tell, were the priors and the underlying algorithm used to find the optimal design.
[…]
The R code I ran was just slightly faster than my Julia code. Because the two packages are using different underlying algorithms to find optimal designs, I don't think this conclusion is very meaningful.

I actually did a small benchmark (that I still need write up properly) of Kirstine.jl vs ICAOD for information matrices and objective functions of two different models, since these are independent of the optimization algorithms. Here, Kirstine.jl is 2--6 times faster than an ICAOD model with C++ objective, and 15 times faster than a pure R objective. If you're interested in the details, I'll put the rough code somewhere accessible.

This is a compliment to the documentation and design of Kirstine.jl

Thanks :)

[sneakers-the-rat]

Fabulous - are there any blockers for you @roualdes that the authors should be working on? I see some conversation in #3 but want to make sure any questions you have are addressed and the authors know what they should be working on here. We're still waiting on @harisorgn to finish a read, so no hurry on anyone's part.

[lsandig]

I actually did a small benchmark (that I still need write up properly) of Kirstine.jl vs ICAOD
[…]
I'll put the rough code somewhere accessible.

FWIW, I set up a repo for collecting additional examples, which I meant to do anyway, and put the slightly cleaned-up benchmark in there.

[roualdes]

No blockers, as far as I can see. The package, doc, and paper look of good quality and I'm happy to sign off on moving forward towards publication.

@sneakers-the-rat, what is the preferred way for a reviewer to signal that they have completed their review and everything looks good?

[harisorgn]

Apologies for the delay, I have finished going over the article, code and documentation. I took several notes along the way and then deleted them as @lsandig had already addressed them elsewhere. In particular I appreciate the well tested & organised codebase and the thorough documentation, which I am hoping should reduce friction even for non-experienced Julia users (now with the accompanying kirstine-examples repository)!

In the end I only had typo-based comments in Issue #4. Happy to sign off for publication too.

[sneakers-the-rat]

Super sorry for the delay on my end - a lot going on over here and still working out my workflow for editing. I see both the checklists as completed, and if there are no further comments then i'll move ahead with post-editorial checks :)

[sneakers-the-rat]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• Check that the archive title, author list, version tag, and the license are correct
• Set archive DOI with @editorialbot set <DOI here> as archive
• Set version with @editorialbot set <version here> as version
• Double check rendering of paper with @editorialbot generate pdf
• Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• Recommend acceptance with @editorialbot recommend-accept

[sneakers-the-rat]

Alright @lsandig see the above post for final tasks - need to make a new tagged release and archive it on zenodo or elsewhere, i'll get started on the rest of the tasks

[sneakers-the-rat]

@editorialbot generate pdf

[sneakers-the-rat]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[sneakers-the-rat]

@editorialbot set v0.6.0 as version

[editorialbot]

Done! version is now v0.6.0

[sneakers-the-rat]

@editorialbot set 10.5281/zenodo.11185430 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.11185430

[sneakers-the-rat]

@editorialbot generate pdf

[editorialbot]

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

[sneakers-the-rat]

Everything looks good to me, about to recommend acceptance - this is my first paper as editor so could EiC check that i've done things right here? Thanks to our reviewers and our authors for their work here :)

[sneakers-the-rat]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

OK DOIs

- 10.1137/141000671 is OK
- 10.1214/ss/1177009939 is OK
- 10.1201/b15054 is OK
- 10.1016/s0169-2607(03)00073-7 is OK
- 10.1016/j.cmpb.2012.05.005 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

- No DOI given, and none found for title: DoseFinding: Planning and Analyzing Dose Finding E...
- No DOI given, and none found for title: ICAOD: Optimal Designs for Nonlinear Statistical M...

INVALID DOIs

- None

[editorialbot]

👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5361, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[crvernon]

Everything looks good to me, about to recommend acceptance - this is my first paper as editor so could EiC check that i've done things right here? Thanks to our reviewers and our authors for their work here :)

No problem @sneakers-the-rat! I'll let you know if anything seems off. Thanks!

[crvernon]

🔍 checking out the following:

• reviewer checklists are completed or addressed
• version set
• archive set
• archive names (including order) and title in archive matches those specified in the paper
• archive uses the same license as the repo and is OSI approved as open source
• archive DOI and version match or redirect to those set by editor in review thread
• paper is error free - grammar and typos
• paper is error free - test links in the paper and bib
• paper is error free - refs preserve capitalization where necessary
• paper is error free - no invalid refs without justification

[crvernon]

This review is very clean @sneakers-the-rat, excellent job editing! I have no recommendations for you at this point accept that you keep up the amazing work!

[crvernon]

@editorialbot accept

[editorialbot]

Doing it live! Attempting automated processing of paper acceptance...

[editorialbot]

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Sandig
  given-names: Ludger
  orcid: "https://orcid.org/0000-0002-3174-3275"
doi: 10.5281/zenodo.11185430
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Sandig
    given-names: Ludger
    orcid: "https://orcid.org/0000-0002-3174-3275"
  date-published: 2024-05-20
  doi: 10.21105/joss.06424
  issn: 2475-9066
  issue: 97
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6424
  title: "Kirstine.jl: A Julia Package for Bayesian Optimal Design of
    Experiments"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06424"
  volume: 9
title: "Kirstine.jl: A Julia Package for Bayesian Optimal Design of
  Experiments"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

[editorialbot]

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

[editorialbot]

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.06424 joss-papers#5362
1. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06424
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

[crvernon]

🥳 Congratulations on your new publication @lsandig! Many thanks to @sneakers-the-rat for editing and @harisorgn and @roualdes for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

This publication was very well done!

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

[editorialbot]

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.06424/status.svg)](https://doi.org/10.21105/joss.06424)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06424">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06424/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06424/status.svg
   :target: https://doi.org/10.21105/joss.06424

This is how it will look in your documentation:

We need your help!

The Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

• Volunteering to review for us sometime in the future. You can add your name to the reviewer list here: https://reviewers.joss.theoj.org/join
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[sneakers-the-rat]

Heck ya thanks to everyone involved <3

[lsandig]

Great news! Thanks to everyone involved for their time!