Joss-reviews: [REVIEW]: mlr3: A modern object-oriented machine learning framework in R

[whedon]

Submitting author: @mllg (Michel Lang)
Repository: https://github.com/mlr-org/mlr3
Version: v0.1.5
Editor: @terrytangyuan
Reviewers: @nhejazi , @osorensen
Archive: 10.5281/zenodo.3569963

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/6cd6b73928c8b71cad58ec1487aea20e"><img src="https://joss.theoj.org/papers/6cd6b73928c8b71cad58ec1487aea20e/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/6cd6b73928c8b71cad58ec1487aea20e/status.svg)](https://joss.theoj.org/papers/6cd6b73928c8b71cad58ec1487aea20e)

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

@nhejazi , 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 @terrytangyuan know.

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

Review checklist for @nhejazi

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 (@mllg) 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 @osorensen

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 (@mllg) 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. @nhejazi 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:

1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

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 to check references...

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v028.i05 is OK
• 10.1145/1656274.1656278 is OK
• 10.5281/zenodo.3541506 is OK
• 10.32614/RJ-2017-028 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

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

[terrytangyuan]

@whedon add @osorensen as reviewer

[whedon]

OK, @osorensen is now a reviewer

[osorensen]

@terrytangyuan , it seems like whedon did not add a review checklist for me. Could you please fix?

[terrytangyuan]

@osorensen Fixed!

[osorensen]

@mllg, the paper is very well written. My only suggestion is to correct the spelling of the word _techniques_ in the sentence:

... integrates many feature filtering technqiues and ...

[mllg]

Thanks, fixed in https://github.com/mlr-org/mlr3/commit/bd32569c234a88a2bb740e26975adaa487eb0de2.

[terrytangyuan]

👋 @nhejazi Would you be able to continue reviewing this soon?

[nhejazi]

Sure @terrytangyuan, I'll complete this review by the end of this week (will be ready prior to Monday, 09 December).

[nhejazi]

@mllg, the mlr3 R package looks quite useful, well-tested, and well-documented (from a design perspective, our own sl3 package https://github.com/tlverse/sl3/ seems to have tried to do something very similar, so it's good to see a more robust project on the same track). To echo @osorensen, the paper is also quite excellently written. You've made the job of reviewing this work very easy!

[terrytangyuan]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v028.i05 is OK
• 10.1145/1656274.1656278 is OK
• 10.5281/zenodo.3541506 is OK
• 10.32614/RJ-2017-028 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[terrytangyuan]

Thanks!

@mllg At this point could you make a new release of this software that includes the changes that have resulted from this review. Then, please make an archive of the software in Zenodo/figshare/other service and update this thread with the DOI of the archive? For the Zenodo/figshare archive, please make sure that:

• The title of the archive is the same as the JOSS paper title
• That the authors of the archive are the same as the JOSS paper authors
  I can then move forward with accepting the submission.

[mllg]

I've released version 0.1.5 on GitHub (https://github.com/mlr-org/mlr3/releases/tag/v0.1.5) and CRAN (https://cran.r-project.org/package=mlr3). The GitHub release is uploaded to Zenodo with DOI 10.5281/zenodo.3569963: https://zenodo.org/record/3569963

[terrytangyuan]

@whedon set v0.1.5 as version

[whedon]

OK. v0.1.5 is the version.

[terrytangyuan]

@whedon set 10.5281/zenodo.3569963 as archive

[whedon]

OK. 10.5281/zenodo.3569963 is the archive.

[terrytangyuan]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.18637/jss.v028.i05 is OK
• 10.1145/1656274.1656278 is OK
• 10.5281/zenodo.3541506 is OK
• 10.32614/RJ-2017-028 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1169

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1169, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[terrytangyuan]

@openjournals/joss-eics The paper looks good to me now! Could you take it from here?

[kyleniemeyer]

looks good to me too!

[kyleniemeyer]

@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/1170
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01903
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...

[kyleniemeyer]

Congrats @mllg on your article's publication in JOSS!

Many thanks to @nhejazi and @osorensen for reviewing, and @terrytangyuan for editing.

[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.01903/status.svg)](https://doi.org/10.21105/joss.01903)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01903">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01903/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01903/status.svg
   :target: https://doi.org/10.21105/joss.01903

This is how it will look in your documentation:

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