[REVIEW]: TDApplied: An R package for machine learning and inference with persistence diagrams

[editorialbot]

Submitting author: !--author-handle-->@shaelebrown<!--end-author-handle-- (Shael Brown) Repository: https://github.com/shaelebrown/TDApplied Branch with paper.md (empty if default branch): JOSS Version: v3.0.3 Editor: !--editor-->@mahfuz05062<!--end-editor-- Reviewers: @EduPH, @peekxc Archive: 10.5281/zenodo.10814141

Status

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Markdown: [![status](https://joss.theoj.org/papers/6ee488680b5273f5ad1d9290709294da/status.svg)](https://joss.theoj.org/papers/6ee488680b5273f5ad1d9290709294da)

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

@EduPH & @peekxc, 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 @mahfuz05062 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 @EduPH

📝 Checklist for @peekxc

[editorialbot]

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

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.08 s (976.6 files/s, 295827.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               32            980           2907           4283
C++                             17            809           2297           4256
C/C++ Header                    16            487           2160           1611
TeX                              2            120              0            891
Rmd                              6            536            820            868
Markdown                         5            185              0            695
YAML                             1              3              4             18
-------------------------------------------------------------------------------
SUM:                            79           3120           8188          12622
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 778

[editorialbot]

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

OK DOIs

- 10.21105/joss.00860 is OK
- 10.1007/s00454-002-2885-2 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1523/eneuro.0543-19.2020 is OK
- 10.32614/rj-2011-002 is OK
- 10.1038/s41598-021-88027-8 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1186/s13244-023-01413-w is OK
- 10.1007/978-3-540-33037-0_14 is OK

MISSING DOIs

- None

INVALID DOIs

- None

[editorialbot]

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

[mahfuz05062]

@EduPH and @peekxc - Thanks for agreeing to review this submission.

This is the review thread for the paper. All of our communications will happen here from now on.

As mentioned above, you can use the command @editorialbot generate my checklist to create your review checklist. 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 (https://joss.readthedocs.io/en/latest/reviewer_guidelines.html)

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, reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention openjournals/joss-reviews#6321 so that a link is created to this thread for visibility. 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 2-4 weeks. Please let me know if you require additional time. We can also use editorialbot (our bot) to set automatic reminders if you know you'll be away for a known period.

Please feel free to ping me (@mahfuz05062) if you have any questions/concerns.

[EduPH]

Review checklist for @EduPH

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/shaelebrown/TDApplied?
• [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 (@shaelebrown) 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?

[mahfuz05062]

Hi @peekxc , I just wanted to make sure that you have noticed this review thread. The instructions are in the first post, but please let me know if you have any questions. Thanks!

[peekxc]

Review checklist for @peekxc

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/shaelebrown/TDApplied?
• [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 (@shaelebrown) 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?

[mahfuz05062]

@peekxc and @EduPH I see that the reviews are moving along nicely! Please keep up the progress and let me know if there is anything I can do to help! Thanks!

[EduPH]

I guess I can add it here. Related to the software paper references. It would be nice to add TDA manuals such as (at least one):

• Computational Topology - an Introduction. H. Edelsbrunner, and J. Harer. American Mathematical Society, (2010)
• Dey TK, Wang Y. Computational Topology for Data Analysis. Cambridge University Press; 2022.
• Carlsson G, Vejdemo-Johansson M. Topological Data Analysis with Applications. Cambridge University Press; 2021.

[mahfuz05062]

I guess I can add it here. Related to the software paper references. It would be nice to add TDA manuals such as (at least one):

• Computational Topology - an Introduction. H. Edelsbrunner, and J. Harer. American Mathematical Society, (2010)
• Dey TK, Wang Y. Computational Topology for Data Analysis. Cambridge University Press; 2022.
• Carlsson G, Vejdemo-Johansson M. Topological Data Analysis with Applications. Cambridge University Press; 2021.

@shaelebrown can you address this? Thanks!

[shaelebrown]

Hi there! Sorry, I am submitting my thesis tomorrow and am very swamped. I've seen all the issues raised and plan on addressing them on Monday if that's alright :)

[mahfuz05062]

Hi there! Sorry, I am submitting my thesis tomorrow and am very swamped. I've seen all the issues raised and plan on addressing them on Monday if that's alright :)

No worries! Good luck with your thesis!

[shaelebrown]

Hey guys I'm back (submitted on Friday :) ), thanks for your patience. @EduPH I added a reference for the TDA with applications manual in the introduction section of the TDApplied Theory and Practice vignette (the sentence starting with "For a broad...") as I am most familiar with that text.

[mahfuz05062]

@peekxc Thanks for completing the review! @EduPH is there anything else you are waiting for? Anything either me or the author can help with? Thanks!

[EduPH]

@mahfuz05062 I've finished checking. Thank you!

[shaelebrown]

@mahfuz05062 what are the next steps at this point?

[mahfuz05062]

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

• Double check authors and affiliations (including ORCIDs)
• Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
• Archive the release on Zenodo/figshare/etc and post the DOI here.
• Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
• Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

• [x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
• [x] Check that the archive title, author list, version tag, and the license are correct
• [x] Set archive DOI with @editorialbot set <DOI here> as archive
• [x] Set version with @editorialbot set <version here> as version
• [x] Double check rendering of paper with @editorialbot generate pdf
• [ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
• [ ] Recommend acceptance with @editorialbot recommend-accept

[mahfuz05062]

@shaelebrown please complete the author tasks listed above (if not already done).

[shaelebrown]

@mahfuz05062 I confirm that:

1. The authors and ORCID ID's are correct.
2. TDApplied version 3.0.3 has been published to CRAN with the updates made in this review process.
3. The zenodo DOI is 10.5281/zenodo.10814141 (https://doi.org/10.5281/zenodo.10814141).
4. The authors and ORCID ID's from the release are correct.
5. The license in the release is correct.

I'll just need to update the paper.md file with those kinds of information, or does that get handled automatically?

[mahfuz05062]

@editorialbot generate pdf

[editorialbot]

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

[mahfuz05062]

@editorialbot set 10.5281/zenodo.10814141 as archive

[editorialbot]

Done! archive is now 10.5281/zenodo.10814141

[mahfuz05062]

@editorialbot set v3.0.3 as version

[editorialbot]

Done! version is now v3.0.3

[mahfuz05062]

@editorialbot generate pdf

[editorialbot]

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

[mahfuz05062]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.00860 is OK
- 10.1007/s00454-002-2885-2 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1523/eneuro.0543-19.2020 is OK
- 10.32614/rj-2011-002 is OK
- 10.1038/s41598-021-88027-8 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1186/s13244-023-01413-w is OK
- 10.1007/978-3-540-33037-0_14 is OK

MISSING DOIs

- No DOI given, and none found for title: TDA: Statistical Tools for Topological Data Analys...
- No DOI given, and none found for title: TDAstats: Pipeline for Topological Data Analysis
- No DOI given, and none found for title: devtools: Tools to Make Developing R Packages Easi...
- No DOI given, and none found for title: Hypothesis testing for topological data analysis
- No DOI given, and none found for title: Persistence Fisher Kernel: A Riemannian Manifold K...

INVALID DOIs

- None

[mahfuz05062]

@shaelebrown Can you check the missing DOI's above? Specially, 'Hypothesis testing for topological data analysis' and 'Persistence Fisher Kernel: A Riemannian ...' should have valid DOIs available as these are journal publications.

[mahfuz05062]

Hi @shaelebrown, did you get a chance to go through the DOI's mentioned above?

[shaelebrown]

Hey @mahfuz05062 sorry I didn't see your message last week - just updated the two DOIs (on the JOSS branch) let me know if that looks better!

[mahfuz05062]

@editorialbot generate pdf

[editorialbot]

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

[mahfuz05062]

@editorialbot check references

[mahfuz05062]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.21105/joss.00860 is OK
- 10.1007/s00454-002-2885-2 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1007/s41468-017-0008-7 is OK
- 10.48550/arXiv.1802.03569 is OK
- 10.1523/eneuro.0543-19.2020 is OK
- 10.32614/rj-2011-002 is OK
- 10.1038/s41598-021-88027-8 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1186/s13244-023-01413-w is OK
- 10.1007/978-3-540-33037-0_14 is OK

MISSING DOIs

- No DOI given, and none found for title: TDA: Statistical Tools for Topological Data Analys...
- No DOI given, and none found for title: TDAstats: Pipeline for Topological Data Analysis
- No DOI given, and none found for title: devtools: Tools to Make Developing R Packages Easi...

INVALID DOIs

- None

[mahfuz05062]

@editorialbot recommend-accept

[editorialbot]

Attempting dry run of processing paper acceptance...

[editorialbot]

:wave: @openjournals/csism-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/5175, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

[editorialbot]

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

OK DOIs

- 10.21105/joss.00860 is OK
- 10.1007/s00454-002-2885-2 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1007/s41468-017-0008-7 is OK
- 10.48550/arXiv.1802.03569 is OK
- 10.1523/eneuro.0543-19.2020 is OK
- 10.32614/rj-2011-002 is OK
- 10.1038/s41598-021-88027-8 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1186/s13244-023-01413-w is OK
- 10.1007/978-3-540-33037-0_14 is OK

MISSING DOIs

- Errored finding suggestions for "TDA: Statistical Tools for Topological Data Analys...", please try later
- No DOI given, and none found for title: TDAstats: Pipeline for Topological Data Analysis
- No DOI given, and none found for title: devtools: Tools to Make Developing R Packages Easi...

INVALID DOIs

- None

[danielskatz]

All - Thanks for the work to this point.

As the AEiC for this track, I'll proofread this tomorrow and get back to @shaelebrown with next steps on their part, if any.

[danielskatz]

@shaelebrown - please change the title of your zenodo deposit to match the title of the paper. This is a change of metadata only, which doesn't require a new deposit or new DOI.

[danielskatz]

@shaelebrown - I've also suggested some small changes in https://github.com/shaelebrown/TDApplied/pull/5 - please merge this, or let me know what you disagree with, then we can proceed.

[shaelebrown]

@danielskatz thanks for the notes - just updated the title to match on zenodo and merged your commits. Let me know if anything still needs fixing!

[danielskatz]

@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

- 10.21105/joss.00860 is OK
- 10.1007/s00454-002-2885-2 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1007/s41468-017-0008-7 is OK
- 10.48550/arXiv.1802.03569 is OK
- 10.1523/eneuro.0543-19.2020 is OK
- 10.32614/rj-2011-002 is OK
- 10.1038/s41598-021-88027-8 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1186/s13244-023-01413-w is OK
- 10.1007/978-3-540-33037-0_14 is OK

MISSING DOIs

- No DOI given, and none found for title: TDA: Statistical Tools for Topological Data Analys...
- No DOI given, and none found for title: TDAstats: Pipeline for Topological Data Analysis
- No DOI given, and none found for title: devtools: Tools to Make Developing R Packages Easi...

INVALID DOIs

- None