[REVIEW]: R for Data Analysis: An open-source resource for teaching and learning analytics with R

whedon commented 1 year ago

Submitting author: @TrevorFrench (Trevor French) Repository: https://github.com/TrevorFrench/R-for-Data-Analysis Version: v1.1.0 Editor: @stats-tgeorge Reviewer: @tomsing1, @corybrunson Archive: 10.5281/zenodo.7896407

:warning: JOSE reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSE is currently operating in a "reduced service mode".

Status

Status badge code:

HTML: <a href="https://jose.theoj.org/papers/5918c67cc21dfcfdca46eb925cec7e45"><img src="https://jose.theoj.org/papers/5918c67cc21dfcfdca46eb925cec7e45/status.svg"></a>
Markdown: [![status](https://jose.theoj.org/papers/5918c67cc21dfcfdca46eb925cec7e45/status.svg)](https://jose.theoj.org/papers/5918c67cc21dfcfdca46eb925cec7e45)

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

@tomsing1 & @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/jose-reviews/invitations

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

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Review checklist for @tomsing1

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 for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
- raised issue
[x] Version: v1.1.0
[x] Authorship: Has the submitting author (@TrevorFrench) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
- This is an online book, and various R packages are referenced and introduced throughout.
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
- The online book appears to be mainly intended for self-study, not for use in a classroom setting. It includes numerous code examples and screenshots, but does not discuss how a teacher might adapt it e.g. for a class.
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support
- raised issue
  Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)
[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
- missing affiliations raised issue
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
- raised issue
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)? online books.
- raised issue

Review checklist for @corybrunson

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 for this learning module available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of a standard license? (OSI-approved for code, Creative Commons for content)
[x] Version: v1.1.0
[x] Authorship: Has the submitting author (@TrevorFrench) made visible contributions to the module? Does the full list of authors seem appropriate and complete?

Documentation

[x] A statement of need: Do the authors clearly state the need for this module and who the target audience is?
[x] Installation instructions: Is there a clearly stated list of dependencies?
[x] Usage: Does the documentation explain how someone would adopt the module, and include examples of how to use it?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the module 2) Report issues or problems with the module 3) Seek support

Pedagogy / Instructional design (Work-in-progress: reviewers, please comment!)

[x] Learning objectives: Does the module make the learning objectives plainly clear? (We don't require explicitly written learning objectives; only that they be evident from content and design.)
[x] Content scope and length: Is the content substantial for learning a given topic? Is the length of the module appropriate?
[x] Pedagogy: Does the module seem easy to follow? Does it observe guidance on cognitive load? (working memory limits of 7 +/- 2 chunks of information)
[x] Content quality: Is the writing of good quality, concise, engaging? Are the code components well crafted? Does the module seem complete?
[x] Instructional design: Is the instructional design deliberate and apparent? For example, exploit worked-example effects; effective multi-media use; low extraneous cognitive load.

JOSE paper

[x] Authors: Does the paper.md file include a list of authors with their affiliations?
[x] A statement of need: Does the paper clearly state the need for this module and who the target audience is?
[x] Description: Does the paper describe the learning materials and sequence?
[x] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
[x] Could someone else teach with this module, given the right expertise?
[x] Does the paper tell the "story" of how the authors came to develop it, or what their expertise is?
[x] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 1 year ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @tomsing1, @corybrunson it looks like you're currently assigned to review this paper :tada:.

:warning: JOSE reduced service mode :warning:

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/jose-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:

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

watching

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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 commented 1 year ago

Wordcount for paper.md is 689

whedon commented 1 year ago

PDF failed to compile for issue #202 with the following error:

 /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:147:in `check_fields': Paper YAML header is missing expected fields: affiliations (RuntimeError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon.rb:89:in `initialize'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `new'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/lib/whedon/processor.rb:38:in `set_paper'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-c5c16aedb3d6/bin/whedon:58:in `prepare'
    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-c5c16aedb3d6/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>'

whedon commented 1 year ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.17 s (354.5 files/s, 164598.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
HTML                            32            933            132          22469
CSS                              4             36             12           1838
JavaScript                      11            200            197           1768
JSON                             9              0              0            794
XML                              1              0              0            131
TeX                              2             10              0            115
YAML                             1              7              0             64
Markdown                         2             33              0             52
-------------------------------------------------------------------------------
SUM:                            62           1219            341          27231
-------------------------------------------------------------------------------

Statistical information for the repository 'b33ad746645384223cfc76cf' was
gathered on 2023/03/14.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Trevor French                    6          6293           4128          100.00

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
Trevor French              2165           34.4          0.2                9.10

whedon commented 1 year ago

Failed to discover a valid open source license.

whedon commented 1 year ago

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

OK DOIs

- None

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ijinfomgt.2016.01.006 is INVALID because of 'https://doi.org/' prefix

whedon commented 1 year ago

:wave: @tomsing1, please update us on how your review is going (this is an automated reminder).

whedon commented 1 year ago

:wave: @corybrunson, please update us on how your review is going (this is an automated reminder).

corybrunson commented 1 year ago

Update: I have not begun my review due to some unexpected obligations, but i expect to begin this week and will try to conclude next week.

tomsing1 commented 1 year ago

@whedon Sorry for the delay, but I have started the review now. My reviewer invite seems to have expired, would you mind reissuing it?

whedon commented 1 year ago

I'm sorry human, I don't understand that. You can see what commands I support by typing:

@whedon commands

tomsing1 commented 1 year ago

@whedon commands

whedon commented 1 year ago

Here are some things you can ask me to do:

# List Whedon's capabilities
@whedon commands

# List of editor GitHub usernames
@whedon list editors

# List of reviewers together with programming language preferences and domain expertise
@whedon list reviewers

EDITORIAL TASKS

# Compile the paper
@whedon generate pdf

# Compile the paper from alternative branch
@whedon generate pdf from branch custom-branch-name

# Ask Whedon to check the references for missing DOIs
@whedon check references

# Ask Whedon to check repository statistics for the submitted software
@whedon check repository

corybrunson commented 1 year ago

@stats-tgeorge could you please clarify whether the "Documentation" section of the checklist refers to the repository / README or to the website / product? My understanding is the former, but i want to be sure before marking items off or raising issues on the repo. Thank you!

stats-tgeorge commented 1 year ago

@corybrunson my understanding is also the repository. Thank you for your weekend work!

tomsing1 commented 1 year ago

@whedon generate pdf

whedon commented 1 year ago

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

corybrunson commented 1 year ago

@stats-tgeorge i'm working through the text and have a positive overall impression of the instructional / pedagogical items on the reviewer checklist. I have one thought on it now, and if it's OK with you i'll add any additional thoughts on it to this comment as i go.

While it hasn't been an issue in any online texts / educational materials i've used so far, i think it's important that they exhibit consistency in style—including tone, educational method, relationship between lessons and examples, etc. Maybe deviations are important in some cases, but in general having a checklist item for consistency would make sense to me. Or maybe consistency should be part of the last item.

tomsing1 commented 1 year ago

@stats-tgeorge My review is complete, and the author has addressed all of the concerns I had raised in their github repository. I was able to confirm that the paper matches the criteria of the checklist, except for (maybe) one:

[ ] Does it describe how it has been used in the classroom or other settings, and how someone might adopt it?
- The author confirmed that this resource is mainly intended for self-study here

Can you advise on how to proceed, please, e.g. whether the author should discuss this in the paper, or if bullet point in the check list can be ignored given the intended use of the resource?

I think this is a useful resource, and recommend publication in JOSE. One more thought:

This learning resource takes on a very large scope - including a basic introduction to R, introductory statistics, plotting, report generation, etc. It currently doesn't tackle a full, real-world examples of an actual Data Analysis, which would add additional value (in my opinion). Such content is not a requirement for publication (according to the checklist / scope of JOSE), but maybe @TrevorFrench could consider it for a future edition.

stats-tgeorge commented 1 year ago

@corybrunson that sounds good. Was that your only question?

stats-tgeorge commented 1 year ago

@tomsing1 I would say they should mention that is the intended use somewhere in their resource. I like the authors suggestion for in their "structure of the book" section. Thank you!

corybrunson commented 1 year ago

@stats-tgeorge my only one so far; if i have more then i'll add them and point back to that comment in my wrap-up comment.

corybrunson commented 1 year ago

@stats-tgeorge i've completed my review and am waiting only for one issue raised by @tomsing1 to be resolved.

tomsing1 commented 1 year ago

@stats-tgeorge and @corybrunson : The final issue has been resolved and my review is complete as well!

stats-tgeorge commented 1 year ago

@openjournals/jose-eics This one is all ready to be accepted.

stats-tgeorge commented 1 year ago

Thank you @tomsing1 and #corybunson for your work!

TrevorFrench commented 1 year ago

@stats-tgeorge I created a new version/release for this which captures all of the changes that were made through the review process. It's now version 1.1.0. Do I need to do anything to update the version on this issue?

stats-tgeorge commented 1 year ago

@TrevorFrench I looked around for it and I see your recent updates on the repo. There is one open issue still. Did that get resolved just not closed out? Issue 22.

TrevorFrench commented 1 year ago

@stats-tgeorge I just resolved issue 22 and updated the release here.

labarba commented 1 year ago

hi @stats-tgeorge 👋 — do run @whedon set v1.1.0 as version after checking the tagged release matches in the target repo.

labarba commented 1 year ago

Next step will be for the author to make an archive on Zenodo and report the DOI here, and the editor to run @whedon set <doi> as archive—the author should make sure to edit the archive metadata so that the title and author list match the JOSE paper. Then finally run @whedon recommend-accept.

TrevorFrench commented 1 year ago

The DOI is: 10.5281/zenodo.7896407

The archive can be found here.

stats-tgeorge commented 1 year ago

@whedon set v1.1.0 as version

whedon commented 1 year ago

OK. v1.1.0 is the version.

stats-tgeorge commented 1 year ago

@whedon set 10.5281/zenodo.7896407 as archive

whedon commented 1 year ago

OK. 10.5281/zenodo.7896407 is the archive.

stats-tgeorge commented 1 year ago

@whedon recommend-accept

whedon commented 1 year ago

Attempting dry run of processing paper acceptance...

whedon commented 1 year ago

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

OK DOIs

- 10.5281/zenodo.3265164 is OK

MISSING DOIs

- None

INVALID DOIs

- https://doi.org/10.1016/j.ijinfomgt.2016.01.006 is INVALID because of 'https://doi.org/' prefix

whedon commented 1 year 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/118

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/jose-papers/pull/118, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

labarba commented 1 year ago

hi @TrevorFrench : please fix the DOI for the Frizzo-Barker reference. The comment from our bot above explains it: remove the URL prefix.

Also, it doesn't quite make sense to cite in the paper the actual learning resource this paper is about. The learning resource will be automatically included as a link in the margin metadata, and also on the landing page of the paper in the JOSE site. You also have a full link at the end of the Summary, which again is redundant to the article metadata linking to the GitHub location of your resource. Consider removing these.

TrevorFrench commented 1 year ago

Hi @labarba -

I removed the doi prefix in this PR and removed the references to the actual resoucre in this PR.

Let me know if that looks alright.

labarba commented 1 year ago

@whedon accept deposit=true

whedon commented 1 year ago

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

whedon commented 1 year 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/123
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/jose.00202
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 1 year ago

Congratulations, @TrevorFrench, your JOSE paper is published! 🚀

Huge thanks to our Editor: @stats-tgeorge, and Reviewers: @tomsing1, @corybrunson — we couldn't do this without you 🙏

whedon commented 1 year 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.00202/status.svg)](https://doi.org/10.21105/jose.00202)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/jose.00202">
  <img src="https://jose.theoj.org/papers/10.21105/jose.00202/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://jose.theoj.org/papers/10.21105/jose.00202/status.svg
   :target: https://doi.org/10.21105/jose.00202

This is how it will look in your documentation:

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