Joss-reviews: [REVIEW]: OnlineStats.jl: A Julia package for statistics on data streams

[whedon]

Submitting author: @joshday (Josh Day)
Repository: https://github.com/joshday/OnlineStats.jl
Version: v1.0.3
Editor: @karthik
Reviewers: @pkofod, @ahwillia
Archive: 10.5281/zenodo.3659245

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/306085f555d2f0015aa1a131e41c491c/status.svg)](https://joss.theoj.org/papers/306085f555d2f0015aa1a131e41c491c)

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

@pkofod & @ahwillia, 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/openjournals/joss-reviews/invitations

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

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

Review checklist for @pkofod

Conflict of interest

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@joshday) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

Review checklist for @ahwillia

Conflict of interest

• [x] 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

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

General checks

• [x] Repository: Is the source code for this software available at the repository url?
• [x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
• [x] Contribution and authorship: Has the submitting author (@joshday) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] 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

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

• [x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• [x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] 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?

[whedon]

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

:star: Important :star:

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

@whedon commands

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

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[karthik]

Editor note: @ahwillia will start review in November.

[whedon]

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

[ahwillia]

This looks good to me -- I went ahead and checked all my boxes. The documentation is really nice, and the functionality of the package is clear.

My only feedback is that it would be nice to show more full-fledged examples or tutorials, since the operations performed by this particular package are nice building blocks for more complex models/applications. Are there any examples of other repos using OnlineStats.jl to do impressive things? Can these be mentioned in the documentation or the README?

Other than this suggestion, I am happy to see this accepted and published as is.

[ahwillia]

Also one area the documentation could use more work is the StatLearn object (e.g. for online fitting of GLMs). An example showing how to take multiple passes over the same dataset (i.e. multiple epochs) could be useful.

[karthik]

@vchuravy Quick ping to check in. Can you give us a sense for when you might complete this review? :pray:

[karthik]

/ooo November 21 until December 2

[ooo[bot]]

:+1: Marked @karthik as OOO from Thursday, November 21st 2019 to Monday, December 2nd 2019. :calendar:

[karthik]

@vchuravy Another ping to check in. Can you give us a sense for when you might complete this review?

[karthik]

@vchuravy Pinging one more time. Are you still able to complete the review?

[karthik]

@joshday Apologies for the delays with this submission. I'm still trying to get a response from reviewer 2. I'll look for a reviewer in the new year. I'll be out of office for the next few weeks.

[karthik]

/ooo December 22 2019 until January 10 2020

[ooo[bot]]

:+1: Marked @karthik as OOO from Sunday, December 22nd 2019 to Friday, January 10th 2020. :calendar:

[karthik]

@joshday I am still looking for reviewers without much success. Are you able to recommend anyone that can review without any conflict of interest?

[pkofod]

@karthik I can review but I do have to disclose that we are both employed by Julia Computing. Though, we do live 7000km from each other, and have never worked on projects together. I have never used OnlineStats.jl either, although I'm aware of it's existence.

[karthik]

@pkofod That's totally fine! In fact I've tried to get a few people from Julia Computing to review. Thanks so much for stepping in, assigning you now.

[karthik]

@whedon remove @vchuravy as reviewer

[whedon]

OK, @vchuravy is no longer a reviewer

[karthik]

@whedon assign @pkofod as reviewer

[whedon]

OK, @pkofod is now a reviewer

[karthik]

@pkofod I have updated the checklist above with your name. Please work through that list. Reviewer guidelines are here: http://joss.theoj.org/about#reviewer_guidelines

[pkofod]

I have looked at the repo for the first part and everything looks fine. It's structured like a typical Julia package, and has docs, CI, a proper readme with examples and a clear indication that contributions are welcome but Josh has strong preference for the design choices. I will try to find time to read the actual paper tomorrow or the day after.

[pkofod]

Everything looks pretty good. There is one thing missing IMO, but it might be a matter of focus and/or intent. Either OnlineStats.jl is mainly seen as a platform for developing online algorithms, and in that case the example is fine: it shows how to implement an algorithm using the structure provided by the package. However, if the goal (as I understood it at least) is mainly to provide implementations, then I think a simple example of using the existing package functionality would be nice. This could/would also show the Plots.jl integration. Just something like the following from the docs would suffice:

o = Partition(Mean())
o2 = Partition(Extrema())

s = Series(o, o2)

fit!(s, y)

plot(s, layout = 1, xlab = "Nobs")

Other than that, lgtm

[karthik]

Thanks @pkofod
@joshday: Can you respond to the comment above:

Either OnlineStats.jl is mainly seen as a platform for developing online algorithms, and in that case the example is fine: it shows how to implement an algorithm using the structure provided by the package. However, if the goal (as I understood it at least) is mainly to provide implementations, then I think a simple example of using the existing package functionality would be nice.

[karthik]

@whedon check references

[karthik]

@whedon generate pdf

[whedon]

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1137/141000671 may be missing for title: Julia: A fresh approach to numerical computing
- https://doi.org/10.1198/0003130042836 may be missing for title: A Tutorial on MM Algorithms

INVALID DOIs

- None

[whedon]

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

[joshday]

In response @ahwillia suggestion, I have added a section to the README about packages that use OnlineStats.

In response to @pkofod:

Either OnlineStats.jl is mainly seen as a platform for developing online algorithms, and in that case the example is fine: it shows how to implement an algorithm using the structure provided by the package. However, if the goal (as I understood it at least) is mainly to provide implementations, then I think a simple example of using the existing package functionality would be nice.

The paper is meant for a more technical audience (the "developing online algorithms" crowd) whereas the documentation is meant for general users. I'm happy to add a higher level example, but I think most people will check the documentation first.

[pkofod]

That makes sense. I'm fine with the current state, just wanted to be sure what the intention was. So looks good to me.

[karthik]

@joshday Can you please check the references and make sure it is parsing correctly?

[joshday]

@karthik I've fixed the reference issues!

[karthik]

@whedon check references

[whedon]

Reference check summary:

OK DOIs

- 10.1137/141000671 is OK

MISSING DOIs

- https://doi.org/10.1007/978-1-4842-3579-9_6 may be missing for title: Spark Streaming

INVALID DOIs

- https://doi.org/10.1137/141000671 is INVALID because of 'https://doi.org/' prefix

[joshday]

I've fixed the invalid DOI.

The "missing" DOI I believe is in error, as I'm citing the actual software. The above DOI is for a book chapter in "Beginning Apache Spark 2", which is not what I'm citing.

[karthik]

If the software doesn't have a DOI, I think we can skip it but I'll tag @arfon in case he can help.

[arfon]

If the software doesn't have a DOI, I think we can skip it but I'll tag @arfon in case he can help.

This sounds fine. The DOI search/recommender is just using the Crossref API looking for similar titles.

[karthik]

@whedon generate pdf

[whedon]

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

[karthik]

LGTM

[karthik]

Ready to accept. Over you to @openjournals/joss-eics

[kthyng]

@joshday Hi! I'll take over from here.

What version number do you want associated with this publication?

Also, can you create an archive of your code at, for example, Zenodo, and report the doi back here? Please be sure that the title and author list match your paper exactly, which might requires editing the metadata.

[karthik]

@kthyng Yikes, sorry I forget about Zenodo and versions. doh.

[joshday]

@kthyng The version I'd like to use is is v1.0.3 and the DOI is 10.5281/zenodo.3659245. Let me know if there's anything else I can do to help!

A big thank you to @ahwillia and @pkofod for reviewing and @karthik for keeping this thing moving along!

[kthyng]

@whedon set v1.0.3 as version

[whedon]

OK. v1.0.3 is the version.

[kthyng]

@whedon set 10.5281/zenodo.3659245 as archive

[whedon]

OK. 10.5281/zenodo.3659245 is the archive.

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Reference check summary:

OK DOIs

- 10.1137/141000671 is OK

MISSING DOIs

- https://doi.org/10.1007/978-1-4842-3579-9_6 may be missing for title: Spark Streaming

INVALID DOIs

- None

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1292

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1292, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[whedon]

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

Here's what you must now do:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1293
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01816
3. If everything looks good, then close this review issue.

4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

   Any issues? notify your editorial technical team...

[kthyng]

Congratulations on your new publication to @joshday!! Thank to editor @karthik and to reviewers @pkofod and @ahwillia — without your time and expertise we couldn't have done this!

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.01816/status.svg)](https://doi.org/10.21105/joss.01816)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01816">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01816/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01816/status.svg
   :target: https://doi.org/10.21105/joss.01816

This is how it will look in your documentation:

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[joshday]

My apologies for missing this in the proof, but a unicode character (μ) fails to render in the example at the end of the paper. Is it possible to revise the paper? I can simply change the problem character to ASCII.

[danielskatz]

Please make the change in the .md or .bib file, than let us know - @arfon will have to manually propagate the change it at this point

[joshday]

Thanks @danielskatz, I've made the change.

[danielskatz]

👋 @arfon - over to you...

[arfon]

👋 @arfon - over to you...

OK this should be updated now. The PDF might take a few hours to show up as modified as there's caching in place for the papers.

[joshday]

Much appreciated! Thank you!