[REVIEW]: quanteda: An R package for the quantitative analysis of textual data

whedon commented 6 years ago

Submitting author: @kbenoit (Kenneth Benoit) Repository: https://github.com/quanteda/quanteda Version: v1.3 Editor: @arfon Reviewer: @lmullen, @borishejblum, @alexgarciac Archive: 10.5281/zenodo.1447219

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

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Review checklist for @lmullen

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?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Version: Does the release version given match the GitHub release (v1.2)?
[x] Authorship: Has the submitting author (@kenbenoit) 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?
[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @borishejblum

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?
[ ] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[ ] Version: Does the release version given match the GitHub release (v1.2)?
[x] Authorship: Has the submitting author (@kenbenoit) 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

[ ] 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?
[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @alexgarciac

Conflict of interest

[ ] 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

[ ] I confirm that I read and will adhere to the JOSS 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?
[ ] Version: Does the release version given match the GitHub release (v1.2)?
[ ] Authorship: Has the submitting author (@kenbenoit) 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 function 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

[ ] Authors: Does the paper.md file include a list of authors with their affiliations?
[ ] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 6 years ago

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

:star: Important :star:

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whedon commented 6 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 6 years ago

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

arfon commented 6 years ago

@lmullen & @alexgarciac - please remember to review this package when you get a chance.

borishejblum commented 6 years ago

My comments are here https://github.com/quanteda/quanteda/issues/1393

kbenoit commented 6 years ago

Just to flag this for the reviewers, in case it makes a difference: Since submission, we have updated the CRAN version to 1.3.4. Looking forward to your reviews.

arfon commented 6 years ago

@lmullen @alexgarciac - do you think you could both complete your reviews this week?

lmullen commented 6 years ago

Will do my best.

On Sun, Jul 22, 2018 at 5:19 PM, Arfon Smith notifications@github.com wrote:

@lmullen https://github.com/lmullen @alexgarciac https://github.com/alexgarciac - do you think you could both complete your reviews this week?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/774#issuecomment-406897506, or mute the thread https://github.com/notifications/unsubscribe-auth/AALNeM9XT9UUA_s1F_uBqrfosKvBQKKCks5uJOxTgaJpZM4Uis2_ .

-- Lincoln Mullen Assistant Professor, Department of History & Art History George Mason University

kbenoit commented 6 years ago

Looking forward to your comments @lmullen @alexgarciac. 😄

lmullen commented 6 years ago

@arfon I am working on this review. Technically I have a conflict of interest according the the JOSS policies, since Ken and I published a JOSS paper together earlier this year. I had assumed that JOSS already knew about this, but I guess not. I do not think this COI should preclude me from submitting my review, but that's your editorial call. What do you think?

arfon commented 6 years ago

@arfon I am working on this review. Technically I have a conflict of interest according the the JOSS policies, since Ken and I published a JOSS paper together earlier this year. I had assumed that JOSS already knew about this, but I guess not. I do not think this COI should preclude me from submitting my review, but that's your editorial call. What do you think?

Thanks for disclosing this @lmullen. As we have multiple reviewers here I'm happy for you to proceed.

arfon commented 6 years ago

:wave: @alexgarciac @lmullen - when do you think you might be able to complete your review by?

lmullen commented 6 years ago

By the end of the day Friday.

On Mon, Sep 10, 2018 at 7:15 AM Arfon Smith notifications@github.com wrote:

👋 @alexgarciac https://github.com/alexgarciac @lmullen https://github.com/lmullen - when do you think you might be able to complete your review by?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/774#issuecomment-419878011, or mute the thread https://github.com/notifications/unsubscribe-auth/AALNePLFahU6TvPVMfINrmK19d3oD6iQks5uZknEgaJpZM4Uis2_ .

-- Lincoln Mullen Assistant Professor, Department of History & Art History George Mason University

lmullen commented 6 years ago

quanteda is an impressive package, well thought out and well implemented. The package is well documented and the test suite is quite extensive.

On the test suite:

The test suite emits numerous warnings. Some of these can obviously be ignored by comparing what is being tested to the warning message. Others, it is not clear why a warning message is being given.
I found at least three test failures, all relating to textplot_wordcloud, with all suggested packages installed.
I installed all the suggested packages listed in the DESCRIPTION. Should the austin package also be listed as a suggested package? Should the wordcloud package?

JOSS specific comments:

The repository does not have "a plain-text LICENSE file" so I have not checked that box. However, following R package convention the license is indicated in the DESCRIPTION, and I don't think there is a need for a separate file.
The version in the repository (1.3.7) is several minor releases ahead of the published CRAN version (1.3.4).
The JOSS paper (at least, based on the PDF proof and on the BibTeX file) does not have DOIs for a number of the articles, though a spot-check confirms that those article have been assigned DOI.

Comments on the text of the paper:

"on entirely sparse operations" should be "entirely on sparse operations"
"quanteda serializes tokens into integers." Is serialization what is happening, or would "hashes" be a better verb?
"make use of the sparseness document-feature matrices": word missing?
Describing families of functions as "textplot" (in quotation marks) seems odd to me. It might be clearer that those are prefixes for the functions by writing something like textplot_*. That format is used later on in the design section.
"These materials help beginner users to understand how to use these functions for basic operations, and expert users to combine the functions for advanced text processing and analysis" should be "These materials help beginner users understand how to use these functions for basic operations and expert users combine the functions for advanced text processing and analysis"
"process large textual data that are difficult for other R packages (such as computing distances or scoring collocations)": This is a misplaced modifier. The "such as" describes analytical computations, not "large textual data." I'd recommend a revision like "perform analyses on large textual data ... such as"
The readtext package should have a citation like the others, even though it is by the same authors.
There are a number of small typographical errors in the PDF proof that should be checked.

arfon commented 6 years ago

The repository does not have "a plain-text LICENSE file" so I have not checked that box. However, following R package convention the license is indicated in the DESCRIPTION, and I don't think there is a need for a separate file.

@kbenoit - please add a plain text LICENSE file that also has a copy of the license. You will then need to tell R CMD check to ignore this by adding LICENSE to your .Rbuildignore file

kbenoit commented 6 years ago

Thanks @arfon, that's easily done and we are happy to work on the other comments and the statement of need. I can also eliminate the local CHECK failures that are caused by tests that try to open graphics devices. Should I consider the reviews complete now, and proceed with the revision?

arfon commented 6 years ago

Should I consider the reviews complete now, and proceed with the revision?

Yes, please go ahead.

kbenoit commented 6 years ago

Please see our revised submission in https://github.com/quanteda/quanteda/pull/1431 in the branch joss-review-response.

@lmullen you are right that the local tests fail (on macOS) anyway for textplot_wordcloud() and this is due to the tests trying to open a graphics device. It does not occur on CI or CRAN, and we will fix this slightly annoying result soon. (https://github.com/quanteda/quanteda/issues/1427)

The warnings from the tests are usually tests of our own warnings, but we will try to clean these up too (https://github.com/quanteda/quanteda/issues/1430).

@alexgarciac we are eager to receive your comments as well, if you have any not already covered by the other two reviewers and @arfon.

kbenoit commented 6 years ago

@arfon what are the next steps?

arfon commented 6 years ago

@lmullen, @borishejblum - could you both confirm that the changes @kbenoit has made in https://github.com/quanteda/quanteda/pull/1431 have addressed your feedback?

lmullen commented 6 years ago

@arfon Yes, I will do this soon.

borishejblum commented 6 years ago

@arfon @kbenoit it seems that my comment regarding the definition of who the target audience is has not been addressed (or did I miss something ?). Thanks

kbenoit commented 6 years ago

@borishejblum We’d be happy to add that. We’re talking to the article or to the README.md on the website? (Or both?)

borishejblum commented 5 years ago

@kbenoit my understanding of JOSS requirements would be both. Thanks

kbenoit commented 5 years ago

@borishejblum please see https://github.com/quanteda/quanteda/pull/1431/commits/78d6ec9e7f000bc20ea27ba8cdad3e814bacff5a

borishejblum commented 5 years ago

Thanks @kbenoit. All my comments have now been succesfully adressed by quanteda's authors.

lmullen commented 5 years ago

I've revised the diffs of the changes and re-run tests, R CMD check, and so on. The improvements to the paper have been made, and the improvements to the local tests in particular make a huge difference for checking the package. I'm satisfied that the changes have been made and the paper can be accepted.

Very much looking forward to citing this paper as I continue to use quanteda in my own work. Congratulations to @kbenoit and team on such fantastic software.

arfon commented 5 years ago

@kbenoit - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.

kbenoit commented 5 years ago

Thanks @arfon (and once again, to all the reviewers for your excellent and supportive comments.

I've updated the release to v1.3.10 (also under CRAN review) and Zenodo has updated the DOI to https://doi.org/10.5281/zenodo.1447219.

arfon commented 5 years ago

@whedon set 10.5281/zenodo.1447219 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.1447219 is the archive.

arfon commented 5 years ago

@lmullen, @borishejblum - many thanks for your reviews here ✨

@kbenoit - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00774 :zap: :rocket: :boom:

whedon commented 5 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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