Joss-reviews: [REVIEW]: rucrdtw: Fast time series subsequence search in R

[whedon]

Submitting author: @pboesu (Philipp Boersch-Supan)
Repository: https://github.com/pboesu/rucrdtw
Version: v0.1.0
Editor: @arfon
Reviewer: @masalmon
Archive: https://dx.doi.org/10.5281/zenodo.164995

Status

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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) 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 questions

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

  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] Version: Does the release version given match the GitHub release (v0.1.0)?

• [x] Authorship: Has the submitting author (@pboesu) made major contributions to the software?

  Functionality

• [x] Installation: Does installation proceed as outlined in the documentation?

• [x] Functionality: Have the functional claims of the software been confirmed?

• [x] Performance: Have any performance claims of the software been confirmed?

  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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?

• [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] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks for JOSS.

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[arfon]

@masalmon - please follow the review guidelines (http://joss.theoj.org/about#reviewer_guidelines) and complete the checklist above as you go. Any questions, please don't hesitate to ask!

[maelle]

@arfon Ok! Will try to do it this or next week :-)

[maelle]

Maybe I only accepted for getting issue number 100 ;-)

[arfon]

Maybe I only accepted for getting issue number 100 ;-)

😆

[noamross]

Reviewer questions

This is a second review.

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).

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] Version: Does the release version given match the GitHub release (v0.1.0)?
• [x] Authorship: Has the submitting author (@pboesu) made major contributions to the software?

Functionality

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

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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

---

Comments:

Thank you for your submission and the opportunity to review this package as a way of learning more about DTW. This is an excellent, compact package that provides bindings to a very useful library. I can see its use as a building block for many applications.

There is one major issue I wish to address here, which is licensing. While the original UCR source code has re-usage comment, I could not locate a _license_ for the original UCR code which is included in this package. This isn't my area of expertise but I want to make sure that re-release under the Apache license is permitted.

As noted above, there is currently no GitHub release of this package.

I have opened issues on the main repository on documentation, testing, and API.

[pboesu]

Thanks @noamross for the review and the constructive feedback! I will try to address the specific issues/pull requests in the coming days.

I did want to respond to the issue of licensing, immediately, though, as this is something I was not 100% certain how to handle at the initial submission. As you note, the original source of the wrapped C++ library is copyrighted, but not licensed. I did contact Eamonn Keogh, the senior author of the original code/paper, prior to making my R wrapper repository public on github and he consented to a public release under the Apache license on github and ultimately CRAN.

[maelle]

Reviewer questions

This is actually the second review, in theory the first one. ;-)

Conflict of interest

• [x] As the reviewer I confirm that there are no conflicts of interest for me to review this work (such as being a major contributor to the software).
  ### 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] Version: Does the release version given match the GitHub release (v0.1.0)?
• [x] Authorship: Has the submitting author (@pboesu) made major contributions to the software?
  ### Functionality
• [x] Installation: Does installation proceed as outlined in the documentation?
• [x] Functionality: Have the functional claims of the software been confirmed?
• [x] Performance: Have any performance claims of the software been confirmed?
  ### Documentation
• [ ] 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.
• [] 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
• [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] References: Do all archival references that should have a DOI list one (e.g. papers, datasets, software)?

Comments:

Thank you for this package!

• I haven't checked the "statement of need" box because I feel there should/could be more details about practical applications.
• There are two examples in the vignette, but they are no "real world" examples, which would really be nice.
• I commented in https://github.com/pboesu/rucrdtw/issues/3 about those two latter points.

[pboesu]

Thank you @masalmon for the review and the PR!

I will try to address all of your comments this week.

[pboesu]

Hi @masalmon and @noamross ,
Thank you again for your constructive reviews! I have now completed my revision of the paper and code.

I believe I have addressed all suggestions, except for adding "real world" examples. A detailed response about the examples, and the other changes to the documentation is here.

I have also responded to the other two issues about a C++ level interface and additional unit tests.

If you are happy with those changes please let me know. I will then tag the release on github to create an archived version on zenodo, and also submit to CRAN.

[maelle]

Hi @pboesu as discussed in the issue in your repo I'm happy with the changes, nice work!

[noamross]

I've examined all of the changes since I first reviewed this package and @pboesu has satisfied all my concerns. I approve!

[pboesu]

Brilliant! Thanks again, @noamross and @masalmon for the constructive review!

I have tagged the release and archived it on zenodo. The archive doi is 10.5281/zenodo.164995.

I also have submitted the package to CRAN.

[arfon]

@noamross and @masalmon many thanks for the reviews here ✨

@pboesu - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00100 🎉 🚀 💥