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

editorialbot commented 6 months ago

Submitting author: !--author-handle-->@marccanby@ajstewartlang<!--end-editor-- Reviewers: @fauxneticien, @SimonGreenhill, @SietzeN Archive: Pending

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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 commented 6 months ago

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editorialbot commented 6 months ago

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
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SUM:                            24            642            642           3538
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 6 months ago

Wordcount for paper.md is 2537

editorialbot commented 6 months ago

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 commented 6 months ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

SimonGreenhill commented 5 months ago

Review checklist for @SimonGreenhill

Conflict of interest

[x] 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

[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 https://github.com/marccanby/linguiphyr/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 5 months ago

Some comments on the manuscript here

SimonGreenhill commented 5 months ago

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 commented 5 months ago

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 commented 5 months ago

Some issues with references: https://github.com/marccanby/linguiphyr/issues/2

SimonGreenhill commented 5 months ago

And some comments / issues on the code:

[x] https://github.com/marccanby/linguiphyr/issues/3
[x] https://github.com/marccanby/linguiphyr/issues/4
[x] https://github.com/marccanby/linguiphyr/issues/5
[x] https://github.com/marccanby/linguiphyr/issues/6
[x] https://github.com/marccanby/linguiphyr/issues/7
[x] 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 commented 4 months ago

@editorialbot add @SietzeN as reviewer

editorialbot commented 4 months ago

@SietzeN added to the reviewers list!

SimonGreenhill commented 4 months ago

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

marccanby commented 4 months ago

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 commented 4 months ago

thanks @marccanby

SietzeN commented 4 months ago

Review checklist for @SietzeN

Conflict of interest

[x] 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

[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 https://github.com/marccanby/linguiphyr/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 4 months ago

Review checklist for @fauxneticien

Conflict of interest

[x] 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

[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 https://github.com/marccanby/linguiphyr/?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] 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?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] 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.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] 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

[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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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 commented 4 months ago

Two minor issues raised for @marccanby in repo: https://github.com/marccanby/linguiphyr/issues/15

SietzeN commented 3 months ago

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

ajstewartlang commented 2 months ago

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

marccanby commented 2 months ago

@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 commented 1 month ago

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.