[REVIEW]: Take a moderndive into introductory linear regression with R

whedon commented 3 years ago

Submitting author: @rudeboybert (Albert Y. Kim) Repository: https://github.com/moderndive/moderndive Version: v0.5.2 Editor: @moorepants Reviewer: @lisamr, @lwjohnst86 Archive: 10.5281/zenodo.5119261

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/ca30a7168bbc1d583a5feb2cc596758d"><img src="https://jose.theoj.org/papers/ca30a7168bbc1d583a5feb2cc596758d/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/ca30a7168bbc1d583a5feb2cc596758d/status.svg)](https://jose.theoj.org/papers/ca30a7168bbc1d583a5feb2cc596758d)

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

@lisamr & @lwjohnst86, 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/jose-reviews/invitations

The reviewer guidelines are available here: https://openjournals.readthedocs.io/en/jose/reviewer_guidelines.html. Any questions/concerns please let @moorepants know.

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

Review checklist for @lisamr

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE 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 JOSE 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: v0.5.2
[x] Authorship: Has the submitting author (@rudeboybert) made substantial 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? (and documentation is sufficient?)
[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 the need for this software 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?
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] 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 the need for this software 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 @lwjohnst86

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSE 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 JOSE 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: v0.5.2
[x] Authorship: Has the submitting author (@rudeboybert) made substantial 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? (and documentation is sufficient?)
[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 the need for this software 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?
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] 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 the need for this software and who the target audience is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

rudeboybert commented 3 years ago

Hi @lisamr,

I just added the Statement of Need to the README: https://github.com/moderndive/moderndive#statement-of-need
I added a note to the documentation for geom_categorical_model() explaining what the solid and dashed lines are in this commit

Many thanks for all your work on this review

lisamr commented 3 years ago

@rudeboybert looks great to me!

lwjohnst86 commented 3 years ago

@rudeboybert I've checked all the boxes though you still have almost identical text ("six features") between your vignette and your README which I think you should de-duplicate, or rather "don't repeat yourself" :wink: Other than that, it looks great!! :grin:

rudeboybert commented 3 years ago

Thanks @lwjohnst86, I will keep the six features text to form a bridge between the README and the manuscript, even at the cost of repeating myself.

@lisamr could you check off the remaining checkbox? After that point I believe @moorepants can move the review to the next phase

lisamr commented 3 years ago

@rudeboybert sorry about that, thought I already checked it off.

moorepants commented 3 years ago

@rudeboybert I've checked over everything, including @lisamr and @lwjohnst86's final sign off and it all looks ready to go!

Next steps:

Create a new release for your github repository and report the tag string here.
Create a Zenodo archive of the release made in point 1 and report the DOI here.

moorepants commented 3 years ago

@whedon check references

whedon commented 3 years ago

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

OK DOIs

- 10.5070/T573020084 is OK
- 10.1080/00224065.2020.1848366 is OK
- 10.21105/joss.01686 is OK
- 10.1007/978-0-387-98141-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

moorepants commented 3 years ago

@whedon check repository

whedon commented 3 years ago

Wordcount for paper.md is 1547

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.06 s (871.4 files/s, 138374.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
SVG                             19              0              0           3446
Markdown                         8            396              0           1391
R                               18            257            810           1013
Rmd                              3            327            571            289
YAML                             6             37              1            266
TeX                              1              9              1             73
Bourne Shell                     1              1              4              1
-------------------------------------------------------------------------------
SUM:                            56           1027           1387           6479
-------------------------------------------------------------------------------

Statistical information for the repository '46ca8f2d5064c97c0f925280' was
gathered on 2021/07/19.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Luke W. Johnston                 1             0            367           36.48
ismayc                           3           187              2           18.79
rudeboybert                      7           316            134           44.73

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments

rudeboybert commented 3 years ago

Hey @moorepants:

I just updated the moderndive package on CRAN to version 0.5.2
I've tagged the release on GitHub here. By tag string I believe you mean v0.5.2
I created a Zenodo archive of the release. The DOI is 10.5281/zenodo.5119261

moorepants commented 3 years ago

@whedon set v0.5.2 as version

whedon commented 3 years ago

OK. v0.5.2 is the version.

moorepants commented 3 years ago

@whedon set 10.5281/zenodo.5119261 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5119261 is the archive.

moorepants commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

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

moorepants commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.5070/T573020084 is OK
- 10.1080/00224065.2020.1848366 is OK
- 10.21105/joss.01686 is OK
- 10.1007/978-0-387-98141-3 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @openjournals/jose-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/jose-papers/pull/61

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/61, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

rudeboybert commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

I'm sorry @rudeboybert, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

moorepants commented 3 years ago

@labarba This paper is ready to be accepted!

@lisamr and @lwjohnst86 thank you very much for your quality review. We at JOSE value your contribution.

@rudeboybert thank you for your patience with this submission. I apologize for losing track of it originally. The paper and software look great and I hope you are pleased with the final reviewed result. This is a very nice addition to the literature. Thanks for submitting to JOSE.

rudeboybert commented 3 years ago

Thank you @labarba and @moorepants for your work sustaining this wonderful initiative. I added my name to your list of potential reviewers awhile back, I hope to contribute someday.

@lisamr and @lwjohnst86 thanks once again for your detailed and thoughtful reviews. It was a pleasure working with you.

moorepants commented 3 years ago

I added my name to your list of potential reviewers awhile back, I hope to contribute someday.

Good to know. We'll reach out for sure.

lwjohnst86 commented 3 years ago

Congrats! :partying_face: and likewise :relaxed:

labarba commented 3 years ago

hi @rudeboybert 👋 — Could you edit the metadata of the Zenodo archive so the title and author list matches the JOSE paper?

rudeboybert commented 3 years ago

Hi @labarba, done: https://zenodo.org/record/5119261

labarba commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

labarba commented 3 years ago

@openjournals/dev — is whedon having a bad day?

whedon commented 3 years ago

PDF failed to compile for issue #115 with the following error:

 /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/abstract_response.rb:249:in `exception_with_response': 500 Internal Server Error (RestClient::InternalServerError)
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/abstract_response.rb:129:in `return!'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:836:in `process_result'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:743:in `block in transmit'
    from /app/vendor/ruby-2.6.6/lib/ruby/2.6.0/net/http.rb:920:in `start'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:727:in `transmit'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:163:in `execute'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient/request.rb:63:in `execute'
    from /app/vendor/bundle/ruby/2.6.0/gems/rest-client-2.1.0/lib/restclient.rb:66:in `get'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/compilers.rb:119:in `pdf_from_markdown'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/compilers.rb:13:in `generate_pdf'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/lib/whedon/processor.rb:99:in `compile'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:88:in `compile'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-b63fc70cc085/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

arfon commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

I'm sorry @arfon, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

arfon commented 3 years ago

@labarba - could you try again now?

labarba commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/jose-papers/pull/62
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00115
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

labarba commented 3 years ago

Congratulations, @rudeboybert, your JOSE paper is published! 🚀 (And thank you for your patience.)

Huge thanks to our Editor: @moorepants, and the Reviewers: @lisamr, @lwjohnst86 — your contributions make this possible 🙏

whedon commented 3 years ago

: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://jose.theoj.org/papers/10.21105/jose.00115/status.svg)](https://doi.org/10.21105/jose.00115)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00115">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00115/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00115/status.svg
   :target: https://doi.org/10.21105/jose.00115

This is how it will look in your documentation:

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