[PRE REVIEW]: DiscreteEntropy.jl: Entropy Estimation of Discrete Random Variables with Julia

[editorialbot]

Submitting author: !--author-handle-->@kellino<!--end-author-handle-- (David Kelly) Repository: https://github.com/kellino/DiscreteEntropy.jl Branch with paper.md (empty if default branch): paper Version: v0.2.0 Editor: !--editor-->@Nikoleta-v3<!--end-editor-- Reviewers: @niyiyu, @nluetts Managing EiC: Daniel S. Katz

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Author instructions

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

@kellino 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 1.90  T=0.03 s (1510.4 files/s, 143223.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           26            649            625           1576
TOML                             5            173              2            718
Markdown                         9             67              0            234
YAML                             5             10             22            176
TeX                              1             11              0             99
-------------------------------------------------------------------------------
SUM:                            46            910            649           2803
-------------------------------------------------------------------------------

Commit count by author:

   209  David Kelly
    24  IlariaLaTorre
    23  =
     5  CompatHelper Julia

[editorialbot]

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

✅ OK DOIs

- 10.1137/1104033 is OK
- 10.1145/3368089.3409748 is OK
- 10.1023/A:1026096204727 is OK
- 10.1162/NECO_a_00266 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Hyperfuzzing: black-box security hypertesting with...
- No DOI given, and none found for title: Entropy Estimates from Insufficient Samplings
- No DOI given, and none found for title: Entropy inference and the James-Stein estimator, w...

❌ MISSING DOIs

- 10.1109/tit.2004.834752 may be a valid DOI for title: Information Theory, Inference, and Learning Algori...
- 10.3390/e23050561 may be a valid DOI for title: Selecting an effective entropy estimator for short...
- 10.7551/mitpress/1120.003.0065 may be a valid DOI for title: Entropy and inference, revisited

❌ INVALID DOIs

- None

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 626

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

:warning: An error happened when generating the pdf.

[danielskatz]

👋 @kellino - note that your paper does not compile. Please follow the example paper and note that you can click on the error above to find out more about it. In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf after making changes to the .md file or when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[kellino]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1137/1104033 is OK
- 10.1145/3368089.3409748 is OK
- 10.1109/tit.2004.834752 is OK
- 10.3390/e23050561 is OK
- 10.1023/A:1026096204727 is OK
- 10.7551/mitpress/1120.003.0065 is OK
- 10.1162/NECO_a_00266 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: Hyperfuzzing: black-box security hypertesting with...
- No DOI given, and none found for title: Entropy Estimates from Insufficient Samplings
- No DOI given, and none found for title: Entropy inference and the James-Stein estimator, w...

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[kellino]

@editorialbot generate pdf

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

infotheory: A C++/Python package for multivariate information theoretic analysis Submitting author: @madvn Handling editor: @poulson (Retired) Reviewers: @ajgates42, @artemyk Similarity score: 0.7116

MDEntropy: Information-Theoretic Analyses for Molecular Dynamics Submitting author: @cxhernandez Handling editor: @arokem (Retired) Reviewers: @anotherjoshsmith Similarity score: 0.7083

OpenGeoSysUncertaintyQuantification.jl: a Julia library implementing an uncertainty quantification toolbox for OpenGeoSys Submitting author: @baxmittens Handling editor: @kanishkan91 (Active) Reviewers: @ziyiyin97, @dannys4 Similarity score: 0.6940

BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits Submitting author: @kungfugo Handling editor: @jarvist (Retired) Reviewers: @meandmytram, @Roger-luo Similarity score: 0.6889

NoisySignalIntegration.jl: A Julia package for uncertainty evaluation of numeric integrals Submitting author: @nluetts Handling editor: @jbytecode (Active) Reviewers: @myousefi2016, @mseri Similarity score: 0.6859

⚠️ 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.

[danielskatz]

👋 @kellino - please add countries to your affiliations when you get a chance

[danielskatz]

👋 @mikemahoney218 - Do you think you could edit this JOSS submission?

[danielskatz]

@editorialbot invite @mikemahoney218 as editor

[editorialbot]

Invitation to edit this submission sent!

[danielskatz]

👋 @mikemahoney218 - just checking again if you can edit this submission

[mikemahoney218]

Sorry @danielskatz , closed the notification intending to reply once I got off a meeting and then never actually replied.

This seems pretty far outside my area of expertise, so I don't think I'd be the best editor for this submission.

[danielskatz]

👋 @Nikoleta-v3 - Do you think you could edit this JOSS submission?

[danielskatz]

@editorialbot invite @Nikoleta-v3 as editor

[editorialbot]

Invitation to edit this submission sent!

[Nikoleta-v3]

Hello! Thank you for the invite. FYI @danielskatz @kellino, I am not an expert in Julia, I have barely used it, but I’m interested in learning more about the language, especially when it comes to packaging. I’d be very happy to edit the submission.

I’ll make sure to find reviewers who are experts in Julia, haha 😄

[Nikoleta-v3]

@editorialbot assign me as editor

[editorialbot]

Assigned! @Nikoleta-v3 is now the editor

[kellino]

@Nikoleta-v3 I've got to confess that I'm no expert on Julia either (this is actually my first package in the language). Hopefully it should be fairly easy to install and use. I'm open to all suggestions for improvements

[Nikoleta-v3]

Well then, it will be a learning experience for both of us! Before we begin a few things @kellino.

(-) After a quick look at the repository, one file that seems to be missing is the contribution guidelines. Here’s an example of a contributions file from a recent publication I was editing: https://forgemia.inra.fr/pherosensor/pherosensor-toolbox/-/blob/main/CONTRIBUTING.rst?ref_type=heads. It's clear and to the point, so you might want to use this as a guide. There are also more detailed examples, such as: https://github.com/damar-wicaksono/uqtestfuns/blob/dev/CONTRIBUTING.MD

Or you could keep it simple, like this one-sentence example: https://github.com/RECeSS-EU-Project/stanscofi/

I’ll leave it up to you. Could you please make sure to include a section on how to run the tests?

(-) With a quick read through the paper, I noticed a few typos. Could you please correct them?

• is a Julia package (Line 6)
• It is well known (Line 11)
• This difficulty has led (Line 12)
• for those who wish (Line 37)

(-) Once you’ve addressed the above comments, could you please visit: https://reviewers.joss.theoj.org and recommend a few reviewers?

Thank you!

[kellino]

@Nikoleta-v3 I've fixed the typos in the paper (thank you for spotting these) and added a CONTRIBUTING.md, AUTHORS.md and CHANGELOG.md. All of these in paper branch for the moment. I've borrowed heavily from pherosensor in terms of stucture. Should I give them a quick acknowledgement at the end? I'll have another look for reviewers either today or tomorrow, but having flicked through the list before, nobody was an obvious fit.

[Nikoleta-v3]

Thank you @kellino!

I've borrowed heavily from pherosensor in terms of stucture. Should I give them a quick acknowledgement at the end?

No harm in acknowledging them 😄 but it's really up to you!

Some of the authors here: https://github.com/openjournals/joss-reviews/issues/7260#issuecomment-2367632334 could also be potential reviewers 😄

[kellino]

@Nikoleta-v3 the projects with the most obvious overlap are the first two in https://github.com/openjournals/joss-reviews/issues/7260#issuecomment-2367632334, though neither of those projects are in Julia. If the author of https://github.com/madvn/infotheory (madvn) agrees to review, perhaps someone else familar with Julia can also be brought on board?

Failing that, any of the reviewers for the first two papers (ajgates42, artemyk, anotherjoshsmith) should definitely have the expertise from the information theory point of view. DiscreteEntropy.jl is intended to be useful rather than groundbreaking. So maybe a reviewer from a Julia project (eg ziyiyin97, dannys4) might also consider lending their expertise.

[Nikoleta-v3]

Thank you @kellino !

[Nikoleta-v3]

👋🏻 @madvn @nluetts @niyiyu @tvwenger would any of you be willing to review this submission for JOSS?

We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

The submission I'd like you to review is titled: "DiscreteEntropy.jl: Entropy Estimation of Discrete Random Variables with Julia ". You can find more information at the top of this Github issue 🆙

Please let me know if you're available 😄 Thank you!

[tvwenger]

@Nikoleta-v3 Thanks for the invite! I am still dealing with my own submission, so I will pass on reviewing this submission. Please keep me in mind for future submissions!

[Nikoleta-v3]

No worries at all and thank you for your reply @tvwenger! Apologies for missing that you have an ongoing submission. Good luck with the paper! 😄

[niyiyu]

@Nikoleta-v3 Thanks for the invitation. I will be happy to review the submission.

[Nikoleta-v3]

@editorialbot add @niyiyu as reviewer

[editorialbot]

@niyiyu added to the reviewers list!

[nluetts]

Hi @Nikoleta-v3 :wave: you can add me as reviewer as well.

[Nikoleta-v3]

@editorialbot add @nluetts as reviewer

[editorialbot]

@nluetts added to the reviewers list!

[Nikoleta-v3]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7334.

[madvn]

@Nikoleta-v3 Thank you for the invite, but unfortunately I'm super busy now and am not able to take this on. I'll do it next time.