[REVIEW]: textNet: Directed, Multiplex, Multimodal Event Network Extraction from Textual Data

[editorialbot]

Submitting author: @ezufall (Elise Zufall)
Repository: https://github.com/ucd-cepb/textNet
Branch with paper.md (empty if default branch):
Version: 1.0.0
Editor: @crvernon
Reviewers: @amatsuo, @stuartyeates, @kbenoit
Archive: Pending

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/0b79101bc77f0a882689e826acb803ac"><img src="https://joss.theoj.org/papers/0b79101bc77f0a882689e826acb803ac/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/0b79101bc77f0a882689e826acb803ac/status.svg)](https://joss.theoj.org/papers/0b79101bc77f0a882689e826acb803ac)

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

@amatsuo & @stuartyeates, 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 @mikemahoney218 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 @stuartyeates

📝 Checklist for @amatsuo

[editorialbot]

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

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.98  T=0.33 s (1116.7 files/s, 386704.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
XML                            329             28            218          85407
Text                             4              3              0          35139
R                               21            364            684           1503
XSD                              1             50             23            985
Rmd                              2            211            231            452
TeX                              1             22              0            232
Markdown                         3             50              0            191
CSV                              1              0              0            148
DTD                              1             24              0             56
YAML                             1              1              5             24
-------------------------------------------------------------------------------
SUM:                           364            753           1161         124137
-------------------------------------------------------------------------------

Commit count by author:

   154	E.J. Zufall
    19	ezufall
    10	Tyler Scott
     6	tylerandrewscott

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1212

✅ The paper includes a Statement of need section

[editorialbot]

License info:

✅ License found: MIT License (Valid open source OSI approved license)

[editorialbot]

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

✅ OK DOIs

- 10.1111/psj.12556 is OK

🟡 SKIP DOIs

- No DOI given, and none found for title: cbail/textnets
- No DOI given, and none found for title: spaCy: Industrial-strength Natural Language Proces...
- No DOI given, and none found for title: igraph: Network Analysis and Visualization
- No DOI given, and none found for title: spacyr: Wrapper to the ’spaCy’ ’NLP’ Library
- No DOI given, and none found for title: dplyr: A Grammar of Data Manipulation
- No DOI given, and none found for title: data.table: Extension of ’data.frame’
- No DOI given, and none found for title: ClearNLP Dependency Labels
- No DOI given, and none found for title: OntoNotes Release 5.0 with OntoNotes DB Tool v0.99...
- No DOI given, and none found for title: Universal POS Tags

❌ MISSING DOIs

- 10.32614/cran.package.manynet may be a valid DOI for title: manynet: Many Ways to  Make, Modify, Map, Mark, an...
- 10.1038/nrn3354 may be a valid DOI for title: Translating upwards: linking the neural and social...
- 10.4135/9781529775501 may be a valid DOI for title: InfraNodus
- 10.32614/cran.package.devtools may be a valid DOI for title: devtools: Tools to Make Developing R Packages Easi...
- 10.32614/cran.package.network may be a valid DOI for title: network: Classes for Relational Data
- 10.32614/cran.package.pdftools may be a valid DOI for title: pdftools: Text Extraction, Rendering and Convertin...
- 10.32614/cran.package.tidyr may be a valid DOI for title: tidyr: Tidy Messy Data
- 10.32614/cran.package.pbapply may be a valid DOI for title: pbapply: Adding Progress Bar to ’*apply’ Functions
- 10.32614/cran.package.ggraph may be a valid DOI for title: ggraph: An Implementation of Grammar of Graphics f...
- 10.32614/cran.package.sna may be a valid DOI for title: sna: Tools for Social Network Analysis
- 10.1093/oxfordhb/9780199842193.013.15 may be a valid DOI for title: VerbNet

❌ INVALID DOIs

- https://doi.org/10.35111/gq1x-j780 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[mikemahoney218]

👋🏼 @ezufall, @amatsuo, @stuartyeates: this is the review thread for the paper. Just about all of our communications will happen here from now on 😄

As a reviewer, the first step is to create a checklist for your review by entering

@editorialbot generate my checklist

as the top of a new comment in this thread.

These checklists contain the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. The first comment in this thread also contains links to the JOSS reviewer guidelines.

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 openjournals/joss-reviews#7615 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 reviews to be completed within about 4 weeks, though obviously with the holidays we're expecting a slightly longer timeframe. Please let me know if you require some more time!

Please feel free to ping me (@mikemahoney218) if you have any questions/concerns.

[mikemahoney218]

And happy holidays and happy new year to everyone -- figured I'd start the review now that we've got two reviewers, but of course there's no expectation you'll be volunteering to review for us on a holiday!

[mikemahoney218]

@editorialbot add @kbenoit as reviewer

Hi all -- @kbenoit has graciously agreed to be our third reviewer! While we can accept a submission on the basis of two reviews, I always prefer to have a third. So, thanks again @kbenoit , and there's a few more instructions over at
#7615 (comment)

[editorialbot]

@kbenoit added to the reviewers list!

[stuartyeates]

Review checklist for @stuartyeates

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

• 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 https://github.com/ucd-cepb/textNet?
• 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 (@ezufall) 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?

[stuartyeates]

Looking over the repo (haven't downloaded or run the code yet):

(a) Two of the three PDFs appear to have been generated using a technique which means they can't be searched. While not a fatal flaw, this makes the contained information considerably less useful and the project as a whole less transparent.

(b) There appears to be no explicit mention that that all code appears to only have been tested on English-language content. Working in an English-only context is not a fatal flaw, but needs to be mentioned as a limitation.

(c) The repo's one line "About" field is empty. This is used by third party tools which will be marginally less useful without this. Copy the first content line from the README.

(d) The first paragraph of the README needs to mention the primary platform (R).

More feedback to come.

[stuartyeates]

Code isn't installing cleanly for me. On a fresh install of R as packaged by my institution:

R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

I needed to manually:

install.packages("reticulate")
install.packages("spacyr")

before the

devtools::install_github('ucd-cepb/textNet')

---

The PDFs

https://github.com/ucd-cepb/textnet/blob/main/vignettes/test_procedures.pdf
https://github.com/ucd-cepb/textnet/blob/main/vignettes/textNet_vignette_2024.pdf

have code examples which are both too long to reliably re-key and not amenable to cutting and pasting from the PDF (at least on my platform Windows / firefox), making them effectively useless.

[amatsuo]

Review checklist for @amatsuo

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

• 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 https://github.com/ucd-cepb/textNet?
• 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 (@ezufall) 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?

[crvernon]

@editorialbot assign me as editor

👋 I am the Associate Editor-in-Chief for this track and will be taking on this submission while your topic editor is on leave for a bit. Feel free to shoot me any questions you may have here.

[editorialbot]

Assigned! @crvernon is now the editor

[ezufall]

Hi @crvernon, just checking in on the process for me. I assume I wait until all reviewers are finished with their comments before addressing the comments or doing revisions?

[crvernon]

👋 @ezufall - you can address the reviewer comments as they come in if you like. This gives reviewers time to provide any additional feedback. Thanks!

[crvernon]

👋 @ezufall, @amatsuo, @stuartyeates, and @kbenoit - please provide a short update here in this thread to the status of your part of the review. Thanks!

[crvernon]

Just a reminder:

👋 @ezufall, @amatsuo, @stuartyeates, and @kbenoit - please provide a short update here in this thread to the status of your part of the review. Thanks!

[kbenoit]

Hi @crvernon et al, apologies for how long this is taking. But I thought that @ezufall might be making changes in response to @stuartyeates before I updated with my own review. I see that's not the sequencing (apparently) so I will get to this on Tuesday (2 days from now).

[ezufall]

Hello all, I likewise was unclear on the sequencing and thought perhaps all reviewers would comment in a single round.

I'm happy to provide an update and apologize for the delay.

We thank Dr. Yeates for the constructive feedback. In response to point (a), we re-rendered the vignette pdfs, which are now amenable to copy and paste. We also thank Dr. Yeates (b) for the recommendation to clarify the scope of our testing, which is currently in English, (c) the recommendation to include README content in the "About" field of the repo, and (d) the need to mention the primary platform (R) in the README. We have now amended the README and "About" field to incorporate points (b), (c), and (d).

We are also grateful for the opportunity to improve the installation instructions. The textNet package suggests, rather than requires, the spacyr package, as it provides an optional wrapper to assist with preprocessing before use of the main tool textnet_extract(). We made this tool optional to add flexibility for the end user so that the main tool can be used without installation of Python, spaCy, or associated dependencies if the user has a different preferred NLP pipeline. We have now added clarification of the installation procedures to the README to assist with the process.

[amatsuo]

@arfon, thanks for the reminder!

Apologies for the delay. I’ve been caught up with other obligations but will be resuming the review shortly. I’ll provide my feedback early/mid next week.

[amatsuo]

I've provided my feedback as issues in the target repository.

[ezufall]

Thank you very much for your comments! We have read the issues raised and will be working to address each of them by May 9.