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[REVIEW]: tidylda: An R Package for Latent Dirichlet Allocation Using ''tidyverse'' Conventions #6800

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editorialbot opened this issue May 28, 2024 · 72 comments
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accepted C++ published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review TeX Track: 5 (DSAIS) Data Science, Artificial Intelligence, and Machine Learning

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editorialbot commented May 28, 2024

Submitting author: @TommyJones (Tommy Jones)
Repository: https://github.com/TommyJones/tidylda
Branch with paper.md (empty if default branch): main
Version: v0.06.999
Editor: @kanishkan91
Reviewers: @maximelenormand, @hassaniazi
Archive: 10.5281/zenodo.12809519

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/04f617f818a4ef71ea7ffa232016216c"><img src="https://joss.theoj.org/papers/04f617f818a4ef71ea7ffa232016216c/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/04f617f818a4ef71ea7ffa232016216c/status.svg)](https://joss.theoj.org/papers/04f617f818a4ef71ea7ffa232016216c)

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

@maximelenormand & @hassaniazi, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review.
First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @kanishkan91 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

Checklists

📝 Checklist for @maximelenormand

📝 Checklist for @hassaniazi

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Hello humans, I'm @editorialbot, a robot that can help you with some common editorial tasks.

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

@editorialbot commands

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

@editorialbot generate pdf

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Software report:

github.com/AlDanial/cloc v 1.90  T=0.03 s (1721.6 files/s, 282165.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               25            988           1408           2647
C++                              4            319            354            664
Markdown                         8            126              0            540
C/C++ Header                     7            186            130            442
Rmd                              5            284            336            404
TeX                              1              4              0            162
YAML                             4             33             12            120
SVG                              1              0              0             18
C                                1              0              0              1
-------------------------------------------------------------------------------
SUM:                            56           1940           2240           4998
-------------------------------------------------------------------------------

Commit count by author:

   437	Tommy Jones
     9	Tommy
     3	Brendan Knapp

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Paper file info:

📄 Wordcount for paper.md is 1518

✅ The paper includes a Statement of need section

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License info:

🟡 License found: Other (Check here for OSI approval)

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.18637/jss.v091.i02 is OK
- 10.18637/jss.v083.b01 is OK
- 10.21105/joss.00774 is OK
- 10.21105/joss.00037 is OK

MISSING DOIs

- No DOI given, and none found for title: text2vec
- No DOI given, and none found for title: textmineR: Functions for Text Mining and Topic Mod...
- No DOI given, and none found for title: lda
- No DOI given, and none found for title: broom: An R Package for Converting Statistical Ana...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: topicmodels:  An R Package for Fitting Topic Model...
- No DOI given, and none found for title: Software Framework for Topic Modelling with Large ...
- No DOI given, and none found for title: Text Mining Infrastructure in R
- No DOI given, and none found for title: MALLET: A Machine Learning for Language Toolkit
- 10.1002/wics.1212 may be a valid DOI for title: The Comprehensive R Archive Network
- No DOI given, and none found for title: Latent Dirichlet Allocation
- No DOI given, and none found for title: Latent Dirichlet Allocation for Natural Language S...
- No DOI given, and none found for title: Conventions for R Modeling Packages
- No DOI given, and none found for title: Tidy data
- No DOI given, and none found for title: Tidymodels

INVALID DOIs

- None

@kanishkan91
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@TommyJones, @maximelenormand, @hassaniazi, This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

For @maximelenormand, @hassaniazi - Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

As you are probably already aware, The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention #6800 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

Thanks in advance and let me know if you have any questions!!

@maximelenormand
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maximelenormand commented May 29, 2024

Review checklist for @maximelenormand

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/TommyJones/tidylda?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@TommyJones) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • 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?

@kanishkan91
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Hi @maximelenormand, @hassaniazi- Just wanted to check in briefly. How's the review going thus far? Do let me know if you need anything from my side with respect to the same.

Thanks for reviewing this manuscript again!

@maximelenormand
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Hi @kanishkan91, everything is going well. I have opened two issues regarding the general checks and documentation. One of them is already closed. I will go more in-depth into the review of functionalities, documentation, and the paper by the end of the month.

@hassaniazi
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hassaniazi commented Jun 22, 2024

Review checklist for @hassaniazi

Conflict of interest

  • I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

General checks

  • Repository: Is the source code for this software available at the https://github.com/TommyJones/tidylda?
  • License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
  • Contribution and authorship: Has the submitting author (@TommyJones) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
  • Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
  • Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
  • Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

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: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
  • 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?

@hassaniazi
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@kanishkan91
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@hassaniazi and @maximelenormand Thanks so much for review comments thus far!

@maximelenormand
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Hi @kanishkan91, I have finished my review. My concerns have been addressed.

@TommyJones
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@editorialbot generate pdf

@TommyJones
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I've made several updates to the paper based on reviewer comments. Thanks @maximelenormand and @hassaniazi for your comments so far!

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@kanishkan91
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kanishkan91 commented Jul 5, 2024

@hassaniazi - Would you mind taking a look over the next few days to see if your issues are also addressed? Thanks in advance!

@TommyJones
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Ok. Those duplicate entries are removed.

@kanishkan91
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@editorialbot recommend-accept

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Attempting dry run of processing paper acceptance...

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

OK DOIs

- 10.21105/joss.01686 is OK
- 10.18637/jss.v091.i02 is OK
- 10.18637/jss.v083.b01 is OK
- 10.21105/joss.00774 is OK
- 10.21105/joss.00037 is OK
- 10.1214/07-aoas114 is OK

MISSING DOIs

- No DOI given, and none found for title: lda
- No DOI given, and none found for title: broom: An R Package for Converting Statistical Ana...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: Software Framework for Topic Modelling with Large ...
- No DOI given, and none found for title: MALLET: A Machine Learning for Language Toolkit
- 10.1002/wics.1212 may be a valid DOI for title: The Comprehensive R Archive Network
- No DOI given, and none found for title: Latent Dirichlet Allocation
- No DOI given, and none found for title: Latent Dirichlet Allocation for Natural Language S...
- No DOI given, and none found for title: Conventions for R Modeling Packages
- No DOI given, and none found for title: Tidy data
- No DOI given, and none found for title: Tidymodels
- No DOI given, and none found for title: text2vec
- No DOI given, and none found for title: The Structural Topic Model and Applied Social Scie...
- 10.32614/cran.package.textminer may be a valid DOI for title: textmineR: Functions for Text Mining and Topic Mod...
- No DOI given, and none found for title: topicmodels:  An R Package for Fitting Topic Model...
- No DOI given, and none found for title: Text Mining Infrastructure in R
- No DOI given, and none found for title: WarpLDA: a Cache Efficient O(1) Algorithm for Late...

INVALID DOIs

- None

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👋 @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof 👉📄 Download article

If the paper PDF and the deposit XML files look good in openjournals/joss-papers#5672, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

@editorialbot editorialbot added the recommend-accept Papers recommended for acceptance in JOSS. label Jul 24, 2024
@kanishkan91
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@TommyJones I have recommended this for acceptance again now. I will be reading through the paper for typos etc. shortly. The AEiC in this submission track will review shortly and if all goes well this will go live soon!

Once again, Big thank you to @hassaniazi and @maximelenormand for reviewing! JOSS is volunteer run and relies heavily on researchers such as yourself.

@TommyJones
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Amazing. Thank you @kanishkan91 for running this process. And big thanks to @hassaniazi and @maximelenormand for your time, effort, and for the helpful comments making the paper and package better. 🎉

@crvernon
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crvernon commented Jul 25, 2024

🔍 checking out the following:

  • reviewer checklists are completed or addressed
  • version set
  • archive set
  • archive names (including order) and title in archive matches those specified in the paper
  • archive uses the same license as the repo and is OSI approved as open source
  • archive DOI and version match or redirect to those set by editor in review thread
  • paper is error free - grammar and typos
  • paper is error free - test links in the paper and bib
  • paper is error free - refs preserve capitalization where necessary
  • paper is error free - no invalid refs without justification

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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@crvernon
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crvernon commented Jul 25, 2024

👋 @TommyJones - I just need you to address the following before I can move to accept:

  • The license specified in your Zenodo archive does not match the one used in your repository. Please edit the metadata in the Zenodo archive to fix this. A new release is not necessary.
  • Your GitHub releases show a version of v0.0.3 but you specify a v1 release in the archive. Could you please clarify?

In the paper:

  • You have equal authorship specified though you are the sole author. Please remove this designation.
  • Is your affiliation correct? "Foundation, USA"
  • LINE 41: there seems to be an extra quote mark in this
  • LINE 156: to maintain consistency with the rest of your paper headings, the "d" in "details" should be capitalized.
  • Ensure that capitalization is preserved in your references. You can do this using curly brackets around what you wish to maintain the formatting of in your bib file. For example, the "D" and "A" should be capitalized in the Jones 2023 reference in "...dirichlet allocation...". And "r" should be capitalized in the Khun 2019 reference. Please sweep through these to confirm this for all.
  • Check for any missing DOI that need to be included in your references as reported in an above comment in this thread. Some may not be available.

I will then move forward with accepting this paper for publication.

@TommyJones
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@crvernon, I've addressed these issues as described below. (Excuse the list. GitHub isn't letting me check boxes in others' comments.)

  • Updated the Zenodo archive license
  • I botched some metadata on my Github release showing an old version as the latest. I've updated it to reflect JOSS as the latest release. Zenodo also defaulted to v1 and I didn't catch it. Updated to the real semantic version, v0.06.999, that is the JOSS accepted version.
  • Removed equal contribution flag.
  • My affiliation is correct.
  • Removed the quote.
  • Updated capitalization in the title.
  • I've used brackets to preserve capitalization in references.
  • I've added every DOI that I can find. Many are still unavailable.

I've pushed the latest version to the repo. Should be good to check again.

Thank you!

@crvernon
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@editorialbot set v0.06.999 as version

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Done! version is now v0.06.999

@crvernon
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@editorialbot generate pdf

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👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@crvernon
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@editorialbot accept

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

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Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

If using GitHub, a Cite this repository menu will appear in the About section, containing both APA and BibTeX formats. When exported to Zotero using a browser plugin, Zotero will automatically create an entry using the information contained in the .cff file.

You can copy the contents for your CITATION.cff file here:

CITATION.cff

cff-version: "1.2.0"
authors:
- family-names: Jones
  given-names: Tommy
  orcid: "https://orcid.org/0000-0001-6457-2452"
doi: 10.5281/zenodo.12809519
message: If you use this software, please cite our article in the
  Journal of Open Source Software.
preferred-citation:
  authors:
  - family-names: Jones
    given-names: Tommy
    orcid: "https://orcid.org/0000-0001-6457-2452"
  date-published: 2024-07-25
  doi: 10.21105/joss.06800
  issn: 2475-9066
  issue: 99
  journal: Journal of Open Source Software
  publisher:
    name: Open Journals
  start: 6800
  title: "tidylda: An R Package for Latent Dirichlet Allocation Using
    'tidyverse' Conventions"
  type: article
  url: "https://joss.theoj.org/papers/10.21105/joss.06800"
  volume: 9
title: "tidylda: An R Package for Latent Dirichlet Allocation Using
  'tidyverse' Conventions"

If the repository is not hosted on GitHub, a .cff file can still be uploaded to set your preferred citation. Users will be able to manually copy and paste the citation.

Find more information on .cff files here and here.

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🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

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🚨🚨🚨 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.06800 joss-papers#5680
  2. Wait five minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.06800
  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...

@editorialbot editorialbot added accepted published Papers published in JOSS labels Jul 25, 2024
@crvernon
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🥳 Congratulations on your new publication @TommyJones! Many thanks to @kanishkan91 for editing and @maximelenormand and @hassaniazi for your time, hard work, and expertise!! JOSS wouldn't be able to function nor succeed without your efforts.

Please consider becoming a reviewer for JOSS if you are not already: https://reviewers.joss.theoj.org/join

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🎉🎉🎉 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.06800/status.svg)](https://doi.org/10.21105/joss.06800)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.06800">
  <img src="https://joss.theoj.org/papers/10.21105/joss.06800/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.06800/status.svg
   :target: https://doi.org/10.21105/joss.06800

This is how it will look in your documentation:

DOI

We need your help!

The 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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TommyJones commented Jul 25, 2024 via email

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sash19 commented Oct 9, 2024

@editorialbot generate my checklist

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@sash19 I can't do that because you are not a reviewer

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