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[REVIEW]: Welcome to the tidyverse #1686
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Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @ldecicco-USGS, @jeffreyhanson it looks like you're currently assigned to review this paper 🎉. ⭐ Important ⭐ 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:
For a list of things I can do to help you, just type:
For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:
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Laura and Jeff: Thank you for agreeing to review Welcome to the Tidyverse. I realize that this is an extremely unusual JOSS submission in that it is not just one package but a suite of packages. So please take additional time to review. For items on the checklist, if anything needs additional work, leave it unchecked and raise an issue on the appropriate repository. Once you are satisfied that the responses to your questions, check items off. Please reach out here or via email with any questions or issues you run into. Thanks in advance. |
@hadley, I'm very sorry if this is a silly question and I don't want to waste your time, but I just wanted to double check if the pdf version of the manuscript linked above has the correct version of your manuscript? I was noticed that the |
@jeffreyhanson oh shoot, somehow we forgot to update the |
@whedon generate pdf |
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Rendered preview is definitely ok now — sorry for the mess up. |
No worries, thanks for fixing it. |
The manuscript "Welcome to the tidyverse" provides an excellent overview of the tidyverse---an ecosystem of R packages that share a vision for data science---and the tidyverse R package---an R package that helps manage this ecosystem---that will serve as a useful introduction for new data scientists. Currently, the tidyverse collection of packages spans eight core packages and twelve non-core packages. The core packages provide tools for importing (readr R package), organizing (tibble R package), manipulating (dplyr, forcats, purr, stringr, tidyr R packages), and visualizing data (ggplot2 R package). The non-core packages provide more specialized functionalities, such as importing and exporting data from specific formats (e.g. feather R package), manipulating specific data types (e.g. lubridate R package), and converting complex and verbose model outputs into simple tabular formats (e.g. broom R package). In my view, the manuscript is well-written for a broad audience. The tidyverse has had a profound influence over data science, and I look forward to seeing where it takes us in the future. I have organized this review into three sections: Major issues, Minor issues, and Assorted comments. To be clear, the issues listed under Assorted comments are incredibly minor and do not substantially affect the quality of the manuscript. As a consequence, they can be ignored if the authors do not think changes are needed. Since the pdf version of the manuscript does not contain line numbers, I will refer to the line numbers as they appear in the source rmarkdown document at the time of writing this review. @karthik, I have a few questions about exactly how some of the criteria in the Reviewer checklist should be applied to this particular submission (see the bold text in the checklist above). Once you've answered those questions, I can begin creating issues on the respective repositories if that's ok? Major issues
Minor issues
Assorted comments
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The paper "Welcome to the tidyverse" is a 3 page introduction to the tidyverse R package. The tidyverse R package includes 8 core packages and other non-core packages. I am familiar with these tools, and my initial reaction was "this paper is entirely too short". Many of my questions on "tidyverse"-ness however were addressed in the link https://principles.tidyverse.org. Perhaps it would be worth moving that link into the introduction. The JOSS review is not just on the 3 page paper, it is on the entire software ecosystem. In this case, that includes a massive amount of useful resources. Each core package has adaquate to excellent documentation and links to external resources. My impression is this will be a useful paper for people to cite when they used tidyverse tools in their analysis. It is a short paper, but contains many useful links and references. I would recommend this paper to be published, but I offer the following impressions (they can be addressed or ignored):
Each individual repo for core tidyverse packages serves as great examples of how to manage a package in a human centered way....if there were a few specific examples for inspiring other package developers to follow, that would be great. |
@karthik can you follow up with the authors on the status here? |
@Kevin-Mattheus-Moerman, so sorry to all the reviewers for the delay. Edits in the works. |
Thank you Mara! |
Hi @jeffreyhanson Thanks so much for this exhaustive checkbox list. Please go ahead with opening issues in respective repos. I realize this is a huge undertaking as this is a large suite of packages. |
@batpigandme No rush, but when possible can you give me a rough timeline for when I should check in with you on revisions? |
Hi @karthik, Do you happen to have a particularly good example of what responding to feedback should look like? Do we need to resolve all the checkboxes. Thanks for your help, and your patience! |
@jeffreyhanson I'm answering a few more questions here.
No need to interpret this super literally. As long as individual packages contain source code for each package, we are good to check this off.
Don't all R packages require a LICENSE file? http://r-pkgs.had.co.nz/description.html#license even when the license itself is mentioned in the README. Can you point me to ones that don't?
That's fine in this case. It's clear that the Tidyverse idea itself is from Hadley, and this collection represents core packages that are part of that philosophy. So in this case I'd say it's perfectly fine that Hadley is not listed as an author on all of the packages. |
@batpigandme Here are a couple of good examples of responses:
Yes. or provide a reasonable explanation for ones that cannot be resolved so that the reviews can respond. |
@karthik (just responding quickly to license question): From R-exts:
We work around this in (e.g.) We include license files in new packages, but we haven't made a systematic effort to include them in all older packages, so this is a good prompt for us to do so. |
Thanks Hadley. I appreciate the work around. |
Thank you so much, @jeffreyhanson and @ldecicco-USGS, for you thoughtful reviews, and, @karthik, for your guidance throughout this process. We've responded to your feedback piece by piece in three markdown documents:
Of course, if you prefer, we're happy to include the bodies of these documents as comments in this issue. Thank you again for your time and patience, and please let us know if there's anything you think we've overlooked, our outstanding items that we need to address. |
The responses look fantastic to me, and now I'm super excited to see the development of the Tidyverse design guide.... 👯 💯 🎉 |
@hadley This would be a good time to archive on Zenodo and share the Zenodo DOI here. Since you have so many authors you should make sure that Zenodo lists them in order before finishing that step. |
Is there any specific zenodo advice for JOSS or is it obvious what I should be doing? One complexity is that the authors of the JOSS paper are the contributing authors across the entire tidyverse, as opposed to the single author (me) of the tidyverse package. |
Or in the interests of simplicity, should I just add the authors of this paper to the tidyverse package? |
Just the authors of this paper. |
Working on it now. While doing so I noticed that the citation you gave me is slightly off — it should be "Welcome to the tidyverse" not "Welcome to the Tidyverse" |
I have reserved 10.5281/zenodo.3547813, and will upload once I have re-assured myself this will definitely be the same as the version that appears on CRAN. |
Ok, published at https://zenodo.org/record/3547813#.XdV2nC3MzUI |
@whedon set 10.5281/zenodo.3547813, as archive |
OK. 10.5281/zenodo.3547813 is the archive. |
This is ready to publish. Over you to @openjournals/joss-eics |
@whedon accept |
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Check final proof 👉 openjournals/joss-papers#1121 If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#1121, then you can now move forward with accepting the submission by compiling again with the flag
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@whedon accept deposit=true |
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🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦 |
🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨 Here's what you must now do:
Any issues? notify your editorial technical team... |
We're just waiting now for the DOI to resolve, should be any minute. In the meantime, congrats to @hadley and the other authors on your new paper!! Thanks to @karthik for editing and for the time and expertise of our reviewers, @ldecicco-USGS and @jeffreyhanson. 🎉 🎉 |
And it's all there now! Congrats again! |
🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉 If you would like to include a link to your paper from your README use the following code snippets:
This is how it will look in your documentation: We need your help! Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:
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Congrats Tidyverse team! 🎉 🎈 |
Thanks everyone — we greatly appreciate all your hard work making this paper happen! |
Submitting author: @hadley (Hadley Wickham)
Repository: http://github.com/tidyverse/tidyverse
Version: v1.3.0
Editor: @karthik
Reviewer: @ldecicco-USGS, @jeffreyhanson
Archive: 10.5281/zenodo.3547813
Status
Status badge code:
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
@ldecicco-USGS & @jeffreyhanson, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:
The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @karthik know.
✨ Please try and complete your review in the next two weeks ✨
Review checklist for @ldecicco-USGS
Conflict of interest
Code of Conduct
General checks
Functionality
Documentation
Software paper
Review checklist for @jeffreyhanson
Conflict of interest
Code of Conduct
General checks
If I understand correctly, my role is to perform these checks for each of the twenty tidyverse packages and also the tidyverse R package. Therefore I have provided information for each item on the checklist below for each package. Please let me know if I have misunderstood anything.
Functionality
Documentation
write_feather
---aliased as the documentation forread_feather
---is missing an example that uses thewrite_feather
function)cache_info
,rerequest
,httr_options
,curl_docs
,set_config
,reset_config
,with_config
,cookies
,set_cookies
,httr_dr
,set_envvar
,get_envvar
,BROWSE
,oauth_endpoints
(endpoints for linkedin, twitter, vimeo, facebook, github, and azure),progress
,use_proxy
,http_type
,user_agent
,verbose
,write_disk
,write_memory
,write_stream
.stream_in
,stream_out
(also verifies internalapply_by_pages
andstream_out_page
functions),serializeJSON
(also verifiespack
andfixNativeSymbol
),flatten
,loadpkg
,rbind_pages
,unbox
.fit_to_timeline
,pretty_dates
(with seconds, minutes, hours, and months for coverage of internalpretty_sec
,pretty_min
,pretty_hour
,pretty_month
functions),semester
,dst
,Date
.set_values
,submit_form
,google_form
), sessions (html_session
,jump_to
,follow_link
,session_history
,back
,*.session
methods), and encoding (guess_encoding
,repair_encoding
).tidyverse_deps
,tidyverse_logo
.I have checked the CODE_OF_CONDUCT, DESCRIPTION, README, .github/*.md and vignette files for these three pieces of information, and listed below which information might be missing for each tidyverse package. The left check box corresponds to (1), the middle check box to (2) and the third check box to (3). Please let me know if I have missed anything.
Software paper
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