Joss-reviews: [REVIEW]: autoplotly: An R package for automatic generation of interactive visualizations for statistical results

Created on 29 Mar 2018 · 40Comments · Source: openjournals/joss-reviews

Submitting author: @terrytangyuan (Yuan Tang)
Repository: https://github.com/terrytangyuan/autoplotly
Version: v0.1.1
Editor: @arfon
Reviewer: @chlalanne, @corybrunson
Archive: 10.5281/zenodo.1221391

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 instructions & questions

@chlalanne & @corybrunson, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

Make sure you're logged in to your GitHub account
Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

The reviewer guidelines are available here: https://joss.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @arfon know.

Review checklist for @chlalanne

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (v0.1.1)?
[x] Authorship: Has the submitting author (@terrytangyuan) 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 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)?

Review checklist for @corybrunson

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: Does the release version given match the GitHub release (v0.1.1)?
[x] Authorship: Has the submitting author (@terrytangyuan) 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 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)?

accepted published recommend-accept review

Source

whedon

All 40 comments

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @chlalanne, it looks like you're currently assigned as the reviewer for this paper :tada:.

:star: Important :star:

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whedon on 29 Mar 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 29 Mar 2018

--> Check article proof :page_facing_up: <--

whedon on 29 Mar 2018

@chlalanne, @corybrunson - please carry out your review in this issue by updating the checklist above and giving feedback in this issue. The reviewer guidelines are available here: http://joss.theoj.org/about#reviewer_guidelines

Any questions/concerns please let me know.

arfon on 29 Mar 2018

Thanks @arfon. Do you know why the references do not show up in the compiled PDF?

terrytangyuan on 29 Mar 2018

@terrytangyuan - I think this is because they're not being cited directly. (You can read how to do that here)

arfon on 29 Mar 2018

Thanks. I just fixed it in master branch of the repo so feel free to recompile the PDF.

terrytangyuan on 29 Mar 2018

@whedon generate pdf

arfon on 29 Mar 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 29 Mar 2018

--> Check article proof :page_facing_up: <--

whedon on 29 Mar 2018

Thank you for your patience @terrytangyuan ! I am beginning my review.

corybrunson on 13 Apr 2018

@terrytangyuan i have a question that i don't think is appropriate as an issue on the submitted repo. It may just reflect my lack of knowledge about software licenses.

autoplotly is licensed under Apache 2.0, which is described as incompatible with GPLv3 (and v2) in this direction. Since ggplot2 and ggfortify are licensed under GPLv2, this seems to present a problem. Can you address that?

corybrunson on 13 Apr 2018

A note on references: Of the works cited (3 packages, one book, and one publication in _The R Journal_), only one has been assigned a DOI (so far as i can tell), and it is missing from the list. That one is Wickham's book on ggplot2.

corybrunson on 13 Apr 2018

@corybrunson Thanks for taking the time to review! I just responded your issues. I've listed out the TODOs below:

[x] Move blogpost to package vignette (with eval = FALSE in .Rmd file)
[x] Add community guidelines to ggfortify and autoplotly repos
[x] Change autoplotly license to GPLv2
[x] Add DOI to ggplot2 book citation

I'll work on them soon.

terrytangyuan on 13 Apr 2018

@corybrunson Note that I am not adding a LICENSE file to the repo though since they are usually not required for R packages. This is a Github rendering issue and I believe they are working on the fix. I will fix the license in DESCRIPTION file only.

terrytangyuan on 13 Apr 2018

👍1

@corybrunson Just finished all the TODOs. Could you review again? Thanks!

terrytangyuan on 13 Apr 2018

@whedon generate pdf

corybrunson on 13 Apr 2018

Attempting PDF compilation. Reticulating splines etc...

whedon on 13 Apr 2018

--> Check article proof :page_facing_up: <--

whedon on 13 Apr 2018

@terrytangyuan Great! Everything looks and works good for me. I have one final suggestion for the README: Now that a vignette is included, the development version might better be installed via:

devtools::install_github("terrytangyuan/autoplotly", build_vignettes = TRUE)

corybrunson on 13 Apr 2018

👍1

@arfon i have concluded my review and recommend acceptance.

corybrunson on 13 Apr 2018

@corybrunson - excellent. Thanks!

@chlalanne - when do you think you might be able to complete your review by?

arfon on 14 Apr 2018

Sorry for the delay. I somewhat messed up with GH notifications. The package looks great and is working out of the box for me. I reviewed the vignette and the test suite, and they look ok to me.

@terrytangyuan I only have a couple a minor comments:

You cited SO as a possible placeholder for reporting issues or seeking help (ISSUE_TEMPLATE.md); maybe you should also indicate that users need to provide a minimal reproducible example, per SO policy, to prevent questions being closed quickly.
You do not mention plotly::ggplotly(), which provides similar facilities but without the ggfortify backend. I would have thought that it would perhaps fit in the last paragraph of you paper.md file.

@arfon I am done with the review and I am happy with the project as it stands.

even4void on 19 Apr 2018

⚡️thanks @chlalanne.

@terrytangyuan - please take a look at @chlalanne's feedback above.

arfon on 19 Apr 2018

Thanks everyone! I've addressed your comments.