[REVIEW]: LinguiPhyR: A Package for Linguistic Phylogenetic Analysis in R

[editorialbot]

Submitting author: @marccanby (Marc Canby)
Repository: https://github.com/marccanby/linguiphyr/
Branch with paper.md (empty if default branch):
Version: v1.0.0
Editor: @ajstewartlang
Reviewers: @fauxneticien, @SimonGreenhill, @SietzeN
Archive: 10.5281/zenodo.13626333

Status

Status badge code:

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Markdown: [![status](https://joss.theoj.org/papers/bd8fa43abc12b217a5e0e446267b9df1/status.svg)](https://joss.theoj.org/papers/bd8fa43abc12b217a5e0e446267b9df1)

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

@fauxneticien & @SimonGreenhill, 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 @ajstewartlang 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 @SimonGreenhill

📝 Checklist for @SietzeN

📝 Checklist for @fauxneticien

[editorialbot]

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

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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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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (816.3 files/s, 164009.0 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               19            497            638           2976
Markdown                         3            120              0            393
TeX                              1             24              0            151
YAML                             1              1              4             18
-------------------------------------------------------------------------------
SUM:                            24            642            642           3538
-------------------------------------------------------------------------------


gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 2537

[editorialbot]

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

OK DOIs

- 10.1111/j.1749-818X.2008.00082.x is OK
- 10.5334/johd.96 is OK
- 10.1126/science.abg0818 is OK

MISSING DOIs

- 10.1371/journal.pone.0180908 may be a valid DOI for title: BEASTling: A software tool for linguistic phylogenetics using BEAST 2
- 10.1016/s0748-3007(02)00147-0 may be a valid DOI for title: Cladistic analysis of languages: Indo-European classification based on lexicostatistical data
- 10.1075/dia.30.2.01bar may be a valid DOI for title: An experimental study comparing linguistic phylogenetic reconstruction methods
- 10.31219/osf.io/fnav8 may be a valid DOI for title: Short vs long stem alternations in Romance verbal inflection: the S-morphome
- 10.1038/sdata.2018.189 may be a valid DOI for title: Global-scale phylogenetic linguistic inference from lexical resources

INVALID DOIs

- https://doi.org/10.1163/22125892-20201000 is INVALID because of 'https://doi.org/' prefix

[editorialbot]

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

[SimonGreenhill]

Review checklist for @SimonGreenhill

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/marccanby/linguiphyr/?
• 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 (@marccanby) 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?

[SimonGreenhill]

Some comments on the manuscript here

[SimonGreenhill]

The paper currently has no "Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems)". The README.md file contains this. Can this be added as a section to the paper as well?

[SimonGreenhill]

There are no contributing guidlines -- can these be added as either a short statement to the README.md or as a CONTRIBUTIONS.md file?

[SimonGreenhill]

Some issues with references: marccanby/linguiphyr#2

[SimonGreenhill]

And some comments / issues on the code:

• UI glitch marccanby/linguiphyr#3
• browse -> upload step is confusing marccanby/linguiphyr#4
• Attempting to run a PAUP* search without generating nexus crashes marccanby/linguiphyr#5
• consider selectively silencing warnings rather than all of them. marccanby/linguiphyr#6
• Implement tests marccanby/linguiphyr#7
• code / paper should link to DOI resolver not journal webpage as this is more reliable e.g. https://onlinelibrary.wiley.com/doi/abs/10.1111/1467-968X.00091 -> https://doi.org/10.1111/1467-968X.00091

[ajstewartlang]

@editorialbot add @SietzeN as reviewer

[editorialbot]

@SietzeN added to the reviewers list!

[SimonGreenhill]

Thanks @marccanby -- all my requested changes have been implemented.

[marccanby]

Responding to the unchecked boxes in Simon's review checklist:

• Example usage: I have added this to the paper by including a screenshot of each of the app's 3 pages (Data Upload, Tree Search, and Analysis) in the relevant sections of the paper. I also clarified in a footnote where the example dataset may be found in the repo. (All of this info is already in the README.)
• Automated tests: In response to another issue, I created automated tests, which run as part of continuous integration, along with R CMD Check.
• Community guidelines: I added a "How to contribute" section to the README, which contains contact information, and instructions on how the community may contribute.

Thanks very much for all of the feedback!

[SimonGreenhill]

thanks @marccanby

[SietzeN]

Review checklist for @SietzeN

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/marccanby/linguiphyr/?
• 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 (@marccanby) 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?

[fauxneticien]

Review checklist for @fauxneticien

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/marccanby/linguiphyr/?
• 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 (@marccanby) 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?

[fauxneticien]

Two minor issues raised for @marccanby in repo: marccanby/linguiphyr#15

[SietzeN]

Hi @marccanby, I have now finished reviewing the package and manuscript. I raised some issues in repo: marccanby/linguiphyr#16

[ajstewartlang]

👋 @marccanby just checking in with you that you're ok working through the issues raised above?

[marccanby]

@ajstewartlang yes, I'm sorry about the delay - end of semester has been very busy - I've read through them but haven't responded yet - I'll take care of it within the next week!

[marccanby]

I have now responded to all of the issues raised above! Please let me know what the next steps are or if there are further questions.

[ajstewartlang]

👋 @fauxneticien @SimonGreenhill @SietzeN can I ask you to review these responses and let me know whether they address the issues you raised?

[editorialbot]

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

[marccanby]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1017/9781316882313 is OK
- 10.1515/9781474463133 is OK
- 10.1146/annurev-linguistics-011619-030507 is OK
- 10.1017/CBO9780511980183 is OK
- 10.48550/arXiv.2308.09060 is OK
- 10.1163/22125892-20201000 is OK
- 10.1371/journal.pcbi.1003537 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1111/j.1749-818X.2008.00082.x is OK
- 10.1111/j.1096-0031.2003.tb00299.x is OK
- 10.1016/s0040-5809(02)00005-9 is OK
- 10.1075/dia.30.2.01bar is OK
- 10.1111/1467-968X.00091 is OK
- 10.1111/1467-968X.12271 is OK
- 10.1038/sdata.2018.189 is OK
- 10.5334/johd.96 is OK
- 10.1126/science.abg0818 is OK

MISSING DOIs

- No DOI given, and none found for title: Phylogenetic analysis using parsimony (PAUP*) 4.0

INVALID DOIs

- None

[marccanby]

@editorialbot generate pdf

[editorialbot]

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

[marccanby]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.1017/9781316882313 is OK
- 10.1515/9781474463133 is OK
- 10.1146/annurev-linguistics-011619-030507 is OK
- 10.1017/CBO9780511980183 is OK
- 10.48550/arXiv.2308.09060 is OK
- 10.1163/22125892-20201000 is OK
- 10.1371/journal.pcbi.1003537 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1111/j.0014-3820.2002.tb00191.x is OK
- 10.1111/j.1749-818X.2008.00082.x is OK
- 10.1111/j.1096-0031.2003.tb00299.x is OK
- 10.1016/s0040-5809(02)00005-9 is OK
- 10.1075/dia.30.2.01bar is OK
- 10.1111/1467-968X.00091 is OK
- 10.1111/1467-968X.12271 is OK
- 10.1038/sdata.2018.189 is OK
- 10.5334/johd.96 is OK
- 10.1126/science.abg0818 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[marccanby]

@ajstewartlang I fixed the references! do we look good to proceed now? what else do you need from me?

[ajstewartlang]

Many thanks @marccanby - and huge thanks to @fauxneticien, @SimonGreenhill, and @SietzeN for your very helpful and insightful reviews!

@marccanby If you could now do the following please, that would be great:

Make a tagged release of the software.

Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)

Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.

Please list the DOI of the archived version here.

[marccanby]

Hi there! I have now done all of this: I made a tagged release as v1.0.0; and archived the software in Zenodo: https://zenodo.org/records/13626333. The title and author list are correct. The DOI is the following: 10.5281/zenodo.13626333.

Please let me know if you need anything else to complete the publication!

[ajstewartlang]

@editorialbot set v1.0.0 as version

[editorialbot]

Done! version is now v1.0.0

[ajstewartlang]

@editorialbot set 10.5281/zenodo.13626333 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.13626333

[ajstewartlang]

@editorialbot generate pdf

[editorialbot]

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

[ajstewartlang]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

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

✅ OK DOIs

- 10.1017/9781316882313 is OK
- 10.1515/9781474463133 is OK
- 10.1146/annurev-linguistics-011619-030507 is OK
- 10.1017/CBO9780511980183 is OK
- 10.48550/arXiv.2308.09060 is OK
- 10.1163/22125892-20201000 is OK
- 10.1371/journal.pcbi.1003537 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1111/j.0014-3820.2002.tb00191.x is OK
- 10.1111/j.1749-818X.2008.00082.x is OK
- 10.1111/j.1096-0031.2003.tb00299.x is OK
- 10.1016/s0040-5809(02)00005-9 is OK
- 10.1075/dia.30.2.01bar is OK
- 10.1111/1467-968X.00091 is OK
- 10.1111/1467-968X.12271 is OK
- 10.1038/sdata.2018.189 is OK
- 10.5334/johd.96 is OK
- 10.1126/science.abg0818 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[editorialbot]

👋 @openjournals/sbcs-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#5840, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[samhforbes]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1017/9781316882313 is OK
- 10.1515/9781474463133 is OK
- 10.1146/annurev-linguistics-011619-030507 is OK
- 10.1017/CBO9780511980183 is OK
- 10.48550/arXiv.2308.09060 is OK
- 10.1163/22125892-20201000 is OK
- 10.1371/journal.pcbi.1003537 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1111/j.0014-3820.2002.tb00191.x is OK
- 10.1111/j.1749-818X.2008.00082.x is OK
- 10.1111/j.1096-0031.2003.tb00299.x is OK
- 10.1016/s0040-5809(02)00005-9 is OK
- 10.1075/dia.30.2.01bar is OK
- 10.1111/1467-968X.00091 is OK
- 10.1111/1467-968X.12271 is OK
- 10.1038/sdata.2018.189 is OK
- 10.5334/johd.96 is OK
- 10.1126/science.abg0818 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- None

[samhforbes]

Hi @marccanby 👋 sbcs-eic here.
This is looking good so far. I hate to ask at this late stage, but the manuscript is a fair bit longer than we'd normally accept. I wonder if you can simplify / generalise the worked example a bit (retaining the text in a vignette or something, rather than just deleting it, because I think it's really valuable).
Do let me know if this is a particular barrier, I don't want this to be a blocking issue, given we're close to the finish line here.

[marccanby]

Sorry for the delay! I have reduced the length to 5 pages now, largely by fixing figure placement and making sentences more concise. Is this acceptable?
I am also happy to remove Figure 2, which I don't think shows very much, but one of the reviewers requested its inclusion, which is why it's in there.
Is there anything else I can do, or is this good to go across the finish line? @samhforbes

[samhforbes]

@editorialbot generate pdf

[editorialbot]

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

[samhforbes]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1017/9781316882313 is OK
- 10.1515/9781474463133 is OK
- 10.1146/annurev-linguistics-011619-030507 is OK
- 10.1017/CBO9780511980183 is OK
- 10.48550/arXiv.2308.09060 is OK
- 10.1163/22125892-20201000 is OK
- 10.1371/journal.pcbi.1003537 is OK
- 10.1371/journal.pone.0180908 is OK
- 10.1111/j.0014-3820.2002.tb00191.x is OK
- 10.1111/j.1749-818X.2008.00082.x is OK
- 10.1111/j.1096-0031.2003.tb00299.x is OK
- 10.1016/s0040-5809(02)00005-9 is OK
- 10.1075/dia.30.2.01bar is OK
- 10.1111/1467-968X.00091 is OK
- 10.1111/1467-968X.12271 is OK
- 10.1038/sdata.2018.189 is OK
- 10.5334/johd.96 is OK
- 10.1126/science.abg0818 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- https://doi.org/10.1111/1467-968X.12289 is INVALID because of 'https://doi.org/' prefix

[samhforbes]

Hi @marccanby under Canby et al there's a repeat of the https://doi.org/ prefix. I think this is the only issue I can see.