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[REVIEW]: Welcome to the tidyverse #1686

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whedon opened this issue Aug 28, 2019 · 101 comments
Closed

[REVIEW]: Welcome to the tidyverse #1686

whedon opened this issue Aug 28, 2019 · 101 comments
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accepted published Papers published in JOSS recommend-accept Papers recommended for acceptance in JOSS. review

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@whedon
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whedon commented Aug 28, 2019

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

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/3457fa44beec99c5585e1edb601cee61"><img src="https://joss.theoj.org/papers/3457fa44beec99c5585e1edb601cee61/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/3457fa44beec99c5585e1edb601cee61/status.svg)](https://joss.theoj.org/papers/3457fa44beec99c5585e1edb601cee61)

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:

  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 @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

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@hadley) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
  • Functionality: Have the functional claims of the software been confirmed?
  • 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

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • 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

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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 @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.

  • Repository: Is the source code for this software available at the repository url?
    • tidyverse
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Contribution and authorship: Has the submitting author (@hadley) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
    • tidyverse

Functionality

  • Installation: Does installation proceed as outlined in the documentation?
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Functionality: Have the functional claims of the software been confirmed?
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2

Documentation

  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
    • broom
    • dplyr
    • feather (documentation for write_feather---aliased as the documentation for read_feather---is missing an example that uses the write_feather function)
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
    • broom
    • dplyr
    • feather
    • forcats
    • ggplot2
    • haven
    • hms
    • httr
    • jsonlite
    • lubridate
    • modelr
    • purr
    • readr
    • rvest
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse
    • xml2
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
    • Although all packages contain automated tests, some of the packages do not appear to have relatively high coverage (i.e. greater than 80%). This might be due to issues due with using continuous integration services (e.g. limited run time, disk space, or bandwidth). I have listed below some functions in tidyverse packages that might benefit from unit tests in case this is helpful.
    • broom
    • dplyr
    • feather (coverage not reported but contains tests for main functions)
    • forcats
    • ggplot2
    • haven
    • hms
    • httr (48% coverage coverage): it might be useful to add tests for the functions: 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.
    • jsonlite (63% coverage coverage): it might be useful to add tests for the functions: stream_in, stream_out (also verifies internal apply_by_pages and stream_out_page functions), serializeJSON (also verifies pack and fixNativeSymbol), flatten, loadpkg, rbind_pages, unbox.
    • lubridate (72% coverage coverage): it might be useful to add tests for the functions: fit_to_timeline, pretty_dates (with seconds, minutes, hours, and months for coverage of internal pretty_sec, pretty_min, pretty_hour, pretty_month functions), semester, dst, Date.
    • modelr
    • purr
    • readr
    • rvest (43% coverage): it might useful to add tests for functions for forms (set_values, submit_form, google_form), sessions (html_session, jump_to, follow_link, session_history, back, *.session methods), and encoding (guess_encoding, repair_encoding).
    • readxl
    • stringr
    • tibble
    • tidyr
    • tidyverse 58% coverage: perhaps it might be useful to add tests for: tidyverse_deps, tidyverse_logo.
    • xml2
  • 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
    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.
    • [x] [x] broom
    • [x] [x] dplyr
    • [x] [ ] feather
    • [x] [x] forcats
    • [x] [x] ggplot2
    • [x] [x] haven
    • [x] [x] hms
    • [x] [ ] httr
    • [x] [ ] jsonlite
    • [x] [x] lubridate
    • [x] [x] modelr
    • [x] [x] purr
    • [x] [x] readr
    • [x] [x] rvest
    • [x] [x] readxl
    • [x] [x] stringr (information available via files in tidyverse/.github when opening new issue)
    • [x] [x] tibble
    • [x] [x] tidyr
    • [x] [x] tidyverse
    • [x] [ ] xml2

Software paper

  • Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
  • A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
  • State of the field: Do the authors describe how this software compares to other commonly-used packages?
  • Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
  • 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
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whedon commented Aug 28, 2019

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:

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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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@whedon
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whedon commented Aug 28, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Aug 28, 2019

@karthik
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karthik commented Aug 28, 2019

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.

@jeffreyhanson
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@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 paper.Rmd file has been updated more recently than the paper.md file in the repository which (if I understand correctly) is being used to generate the pdf version of the manuscript (e.g. line 117 of the documents are different).

@hadley
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hadley commented Sep 6, 2019

@jeffreyhanson oh shoot, somehow we forgot to update the .md. Let me try and figure out what's gone wrong.

@hadley
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hadley commented Sep 6, 2019

@whedon generate pdf

@whedon
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whedon commented Sep 6, 2019

Attempting PDF compilation. Reticulating splines etc...

@whedon
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whedon commented Sep 6, 2019

@hadley
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hadley commented Sep 6, 2019

Rendered preview is definitely ok now — sorry for the mess up.

@jeffreyhanson
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No worries, thanks for fixing it.

@jeffreyhanson
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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

  • Lines 115--131: In my opinion, the tidyverse R package provides two additional functionalities that are not discussed in the manuscript. Firstly, attaching the tidyverse R package will ensure that tidyverse packages are attached in the correct order. This is not trivial for beginners (e.g. attaching the plyr and dplyr R packages in the incorrect order will cause issues). Secondly, attaching the tidyverse R package will inform the user about namespace conflicts in a concise and informative manner. This is very useful when many tidyverse and non-tidyverse packages are attached. For instance, conflicts arise when the tidyverse R package is attached following the raster R package because both the tidyr R package---a core tidyverse package---and the raster R package contain extract() functions. I think the tidyverse R package is exceptionally useful when evaluated on its standalone merits---that is, disregarding the usefulness of the other packages that comprise the tidyverse---and I think readers would benefit from knowing about these functionalities.

Minor issues

  • Line 109: Perhaps it is worth providing a citation for R? I realize that many readers will likely already be familiar with R to some extent, but perhaps this be useful for readers that are less familiar with R?
  • Lines 109--113: This manuscript is about describing (i) the collection of packages referred to as the tidyverse (covered in the Components and Philosophy sections) and (ii) the tidyverse R package (covered in the Tidyverse package section). The Summary section does a fantastic job of summarizing the tidyverse collection of packages but I feel like it could provide more information about the tidyverse R package itself. Perhaps the purpose of the tidyverse R package could be mentioned in the Summary section?
  • Lines 123--129: Is the tidyverse R package not a core tidyverse package? It is not listed as a core package in Line 129. Maybe it would be useful to explicitly state if the tidyverse R package is a core package or not?
  • Line 131: I wonder if it is worth listing all of the non-core packages in the tidyverse? I suggest this for two reasons. Firstly, it is noted that one of the main purposes for the tidyverse R package is that it provides a convenient method to install all of the packages in the tidyverse. Since there over ten non-core packages listed on the tidyverse package's REAMDE file, I suspect that listing all of these packages here would help the reader appreciate this functionality. Secondly, if one of the main aims of this manuscript is to describe the tidyverse, then I think it would be useful to list all of the packages that comprise the tidyverse. Although additional packages may be added to the tidyverse in the future, I think this would helpful to the reader.
  • Throughout manuscript: The Reviewer Checklist requires that "the authors describe how this software compares to other commonly-used packages". This manuscript does not make such comparisons. For instance, the tidyverse readr R package provides functions for importing data similar to the utils (read.table()) and data.table R packages. If this manuscript were specifically about the readr R package then I would expect such comparisons to be present, but I personally think that detailed comparisons for all tidyverse packages would distract from the main purpose of the manuscript. I raise this issue here because it is on the checklist.

Assorted comments

  • Line 111: ", not to solve every possible problem". Perhaps a semicolon or em-dash would be more appropriate here than a comma?
  • Line 117: Perhaps "downloading and installing" might be more appropriate than "downloading", since the following R code uses install.packages?
  • Line 129: Perhaps "tidyverse version 1.2.0" to make it clear that this sentence is referring to a specific version of the tidyverse R package?
  • Line 129: Is the ordering of these packages significant? If not, perhaps these packages could be listed alphabetically?
  • Line 139: Perhaps "application programming interface (API)" instead of "API" for clarity?
  • Line 139: This is a bit nitpicky but I do not think that data are necessarily "stored" in an API? I would say that data are accessed through an API? Apologies if I'm just plain wrong.
  • Line 139: My impression is that terms like "data frame" and "flat file" will be very useful for individuals with experience in programming R, Python, or SQL. If such individuals are the intended audience for this manuscript, then using such terminology is ideal. If a broader audience is intended, then perhaps using different terms (or clarifying these terms) will be useful (e.g. terms like "tabular" or "spreadsheet" may be more informative for a broader audience).
  • Lines 139 and 141: It appears that the term "data" is being used to refer to a singular entity, though some would argue that the term "data" is a plural. I do not know the grammar rules to which this journal subscribes, so I thought I would raise this point just in case.
  • Line 139: Perhaps it might be useful to provide the full name of the format that corresponds to these file extensions (e.g. tab-separated values for tsv)?
  • Line 139: I don't want to wade into the debate regarding if data is a singular or plural term, but I think that it might be useful to be consistent throughout the manuscript. My interpretation of the sentence containing the phrase "[...] import data stored in other common formats or retrieve it directly [...]" uses the term "data" to refer to both a plural and a singular entity. Perhaps the sentence might be clearer if written as something like "[...] import data from other common formats or the web directly"?
  • Line 139 and elsewhere: The manuscript contains many embedded links which mean that URLs are not shown in the text (e.g. like this). I am not familiar enough with the correct reference style for this journal, so I thought I would raise this point just in case.
  • Line 141: Perhaps "core tidyr package provides" might be useful to be consistent with the rest of the manuscript (e.g. "the core readr package", line 139)?
  • References: The reference for Bache & Wickham (2014) has a lower case "r" in the title when referring to the R programming language.

@ldecicco-USGS
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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):

  1. Discussing the pros and cons of using the "tidyverse" package versus loading individual packages would be useful. It is stated that the "tidyverse" is intended for the general workflow of a data project. However, it might be worth mentioning that it probably is not ideal for using as a dependency in package development. I'm sure there are other examples and issues that should be considered.

  2. Related to #1... I think it would be useful to have a sentence or two addressing using tidyverse as it relates to package development. The tidyverse is such a nice introduction to R....and then the new-tidyverse user becomes a little more confident and wants to make an R package...The first thing they do is wrap their tidyverse code into some functions. Alerting them to some of the considerations would be great. Perhaps a link to http://r-pkgs.had.co.nz and https://dplyr.tidyverse.org/articles/programming.html (there are probably other great resources...those are the 2 I've used over the years).

  3. Listing the full list of dependencies somehow would be useful (either directly in the text, or an obvious link). It might be worth addressing the fact that...yes...there are a lot of packages...but using the "tidyverse" package does simplify installation and helps prevent conflicts. Basically, having a reference to pass on to help ease the weary "IT admin" who has a knee jerk reaction to installing anything with too many dependencies would be great.

  4. Consider adding a link to data.tables, fst, and feather in the sentence "Additional non-core packages".

  5. This is a bit more far-fetched, and could easily be considered out of scope of this paper....but... This might be a good venue for laying out some of the lessons learned over the years from developing all these packages. For example, how and when does the tidyverse team decide to break backwards compatibility? It might be nice to hear more about how to make a package more human centered. The last paragraph lays out some general ideas, but are there specific tactics for package developers to coordinate all that feedback that you all recommend? (I can only imagine that project management is critical for all these packages to be coordinated so well....)

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.

@Kevin-Mattheus-Moerman
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@karthik can you follow up with the authors on the status here?

@batpigandme
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@Kevin-Mattheus-Moerman, so sorry to all the reviewers for the delay. Edits in the works.

@karthik
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karthik commented Oct 16, 2019

Thank you Mara!

@karthik
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karthik commented Oct 16, 2019

@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?

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.

@karthik
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karthik commented Oct 28, 2019

@batpigandme No rush, but when possible can you give me a rough timeline for when I should check in with you on revisions?

@batpigandme
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Hi @karthik,
We have team work week this week, but it's high on our priority list, and we're aiming to finish up next week.

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!

@karthik
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karthik commented Oct 29, 2019

@jeffreyhanson I'm answering a few more questions here.

This repository contains the source code for the tidyverse R package. It does not contain the source code for all the tidyverse packages. However, the README file in this repository contains links to other GitHub repositories which contain the tidyverse packages. Personally, I believe this approach is more sensible than using a single repository for all tidyverse packages, but this particular approach is technically not acceptable based on my (super literal) interpretation of this criteria. @karthik, how should I proceed?

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.

Although not all tidyverse packages contain a LICENSE file, it is worth mentioning that all tidyverse packages contain a DESCRIPTION file which indicates the software license by name. @karthik, do all packages still require a LICENSE file?

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?

I have checked whether the submitting author is listed as an author in the DESCRIPTION file of each tidyverse package. I did not differentiate based on the role (e.g. aut, cre, ctb). @karthik, since this particular submission pertains to a collection of packages is it acceptable if @hadley is not an author of every single package?

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.

@karthik
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karthik commented Oct 29, 2019

@batpigandme Here are a couple of good examples of responses:

#964
#741

Do we need to resolve all the checkboxes.

Yes. or provide a reasonable explanation for ones that cannot be resolved so that the reviews can respond.

@hadley
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hadley commented Oct 30, 2019

@karthik (just responding quickly to license question): From R-exts:

Whereas you should feel free to include a license file in your source distribution, please do not arrange to install yet another copy of the GNU COPYING or COPYING.LIB files but refer to the copies on https://www.R-project.org/Licenses/ and included in the R distribution (in directory share/licenses). Since files named LICENSE or LICENCE will be installed, do not use these names for standard license files. To include comments about the licensing rather than the body of a license, use a file named something like LICENSE.note.

We work around this in (e.g.) use_gpl_license() by including a .Rbuildignored LICENSE.md which R CMD check don't see locally and isn't included in the package bundle (and still allows you to use LICENSE for the (e.g.) template fields needed for to make the MIT license compatible with CRAN's requirements.)

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.

@karthik
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karthik commented Oct 30, 2019

Thanks Hadley. I appreciate the work around.

@batpigandme
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Thank you so much, @jeffreyhanson and @ldecicco-USGS, for you thoughtful reviews, and, @karthik, for your guidance throughout this process.
Your input has made the paper much stronger.

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.

@ldecicco-USGS
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The responses look fantastic to me, and now I'm super excited to see the development of the Tidyverse design guide.... 👯 💯 🎉

@karthik
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karthik commented Nov 19, 2019

@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.

@hadley
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hadley commented Nov 19, 2019

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.

@hadley
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hadley commented Nov 19, 2019

Or in the interests of simplicity, should I just add the authors of this paper to the tidyverse package?

@karthik
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karthik commented Nov 19, 2019

Just the authors of this paper.

@hadley
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hadley commented Nov 19, 2019

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"

@hadley
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hadley commented Nov 19, 2019

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.

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hadley commented Nov 20, 2019

Ok, published at https://zenodo.org/record/3547813#.XdV2nC3MzUI

@karthik
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karthik commented Nov 20, 2019

@whedon set 10.5281/zenodo.3547813, as archive

@whedon
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whedon commented Nov 20, 2019

OK. 10.5281/zenodo.3547813 is the archive.

@karthik
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karthik commented Nov 20, 2019

This is ready to publish. Over you to @openjournals/joss-eics

@kthyng
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kthyng commented Nov 21, 2019

@whedon accept

@whedon
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whedon commented Nov 21, 2019

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Nov 21, 2019

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 deposit=true e.g.

@whedon accept deposit=true

@whedon
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whedon commented Nov 21, 2019


OK DOIs

- 10.1007/0-387-28695-0 is OK

MISSING DOIs

- None

INVALID DOIs

- None

@kthyng
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kthyng commented Nov 21, 2019

@whedon accept deposit=true

@whedon
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whedon commented Nov 21, 2019

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

@whedon
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whedon commented Nov 21, 2019

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented Nov 21, 2019

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.01686 joss-papers#1122
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01686
  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...

@kthyng
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kthyng commented Nov 21, 2019

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. 🎉 🎉

@kthyng
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kthyng commented Nov 21, 2019

And it's all there now! Congrats again!

@kthyng kthyng closed this as completed Nov 21, 2019
@whedon
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whedon commented Nov 21, 2019

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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.01686/status.svg)](https://doi.org/10.21105/joss.01686)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01686">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01686/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01686/status.svg
   :target: https://doi.org/10.21105/joss.01686

This is how it will look in your documentation:

DOI

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:

@karthik
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karthik commented Nov 21, 2019

Congrats Tidyverse team! 🎉 🎈

https://joss.theoj.org/papers/10.21105/joss.01686

@hadley
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hadley commented Nov 21, 2019

Thanks everyone — we greatly appreciate all your hard work making this paper happen!

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