[PRE REVIEW]: TDAvec: An R Package for Computing Vector Summaries of Persistence Diagrams for Topological Data Analysis

[editorialbot]

Submitting author: !--author-handle-->@uislambekov<!--end-author-handle-- (Umar Islambekov) Repository: https://github.com/uislambekov/TDAvec Branch with paper.md (empty if default branch): Version: v0.1.3 Editor: Pending Reviewers: Pending Managing EiC: Daniel S. Katz

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[editorialbot]

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

OK DOIs

- 10.21105/joss.00860 is OK
- 10.1007/s41468-021-00071-5 is OK

MISSING DOIs

- 10.1007/978-3-540-33259-6_7 may be a valid DOI for title: Computational topology: an introduction
- No DOI given, and none found for title: Statistical topological data analysis using persis...
- 10.1145/2582112.2582128 may be a valid DOI for title: Stochastic convergence of persistence landscapes a...
- No DOI given, and none found for title: Persistence images: A stable vector representation...
- No DOI given, and none found for title: Topology and Data
- 10.1007/s10444-021-09893-4 may be a valid DOI for title: Persistence curves: A canonical framework for summ...
- 10.3389/frai.2021.667963 may be a valid DOI for title: An introduction to topological data analysis: fund...
- 10.3389/frai.2021.681108 may be a valid DOI for title: A survey of topological machine learning methods
- 10.32614/cran.package.tdavec may be a valid DOI for title: TDAvec: Vector Summaries of Persistence Diagrams
- No DOI given, and none found for title: TDA: Statistical Tools for Topological Data Analys...
- No DOI given, and none found for title: kernelTDA: Statistical Learning with Kernel for Pe...
- No DOI given, and none found for title: TDAmapper: Topological Data Analysis using Mapper
- 10.32614/cran.package.tdakit may be a valid DOI for title: TDAkit: Toolkit for Topological Data Analysis
- 10.32614/cran.package.tdaunif may be a valid DOI for title: tdaunif: Uniform Manifold Samplers for Topological...
- 10.32614/cran.package.tdapplied may be a valid DOI for title: TDApplied: Machine Learning and Inference for Topo...
- 10.32614/cran.package.ripserr may be a valid DOI for title: ripserr: Calculate Persistent Homology with Ripser...
- 10.1016/j.patcog.2020.107509 may be a valid DOI for title: On the stability of persistent entropy and new sum...
- 10.1016/j.patrec.2014.07.001 may be a valid DOI for title: Efficient classification using the Euler character...
- No DOI given, and none found for title: A computationally efficient framework for vector r...
- 10.1007/978-3-642-40193-0_6 may be a valid DOI for title: Simplicial models and topological inference in bio...
- No DOI given, and none found for title: ggplot2: Elegant Graphics for Data Analysis
- No DOI given, and none found for title: Rcpp: Seamless R and C++ Integration

INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.01 s (1119.1 files/s, 96802.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
C++                              9             59             21            506
TeX                              1             24              0            204
Markdown                         2             24              0            102
Rmd                              1             57            105             74
R                                1              9              2             24
-------------------------------------------------------------------------------
SUM:                            14            173            128            910
-------------------------------------------------------------------------------

Commit count by author:

     8  Umar Islambekov
     1  uislambekov

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 1390

✅ The paper includes a Statement of need section

[editorialbot]

License info:

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

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

TDAstats: R pipeline for computing persistent homology in topological data analysis Submitting author: @rrrlw Handling editor: @leeper (Retired) Reviewers: @corybrunson Similarity score: 0.6908

Ripser.py: A Lean Persistent Homology Library for Python Submitting author: @sauln Handling editor: @arokem (Retired) Reviewers: @lmcinnes Similarity score: 0.6768

Ripserer.jl: flexible and efficient persistent homology computation in Julia Submitting author: @mtsch Handling editor: @VivianePons (Retired) Reviewers: @juliohm, @sauln Similarity score: 0.6622

DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates Submitting author: @LuisScoccola Handling editor: @fabian-s (Active) Reviewers: @mtsch, @raphaelreinauer Similarity score: 0.6436

Akmedoids R package for generating directionally-homogeneous clusters of longitudinal data sets Submitting author: @MAnalytics Handling editor: @karthik (Retired) Reviewers: @karthik, @njtierney Similarity score: 0.6431

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[danielskatz]

👋 @uislambekov - Thanks for your submission.

Due to the relatively small amount of code, the editors will now discuss if it meets the substantial scholarly effort criterion for review by JOSS. You should hear back in a week or so.

In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

[danielskatz]

@editorialbot query scope

[editorialbot]

Submission flagged for editorial review.

[uislambekov]

@editorialbot check references

On Thu, Aug 8, 2024 at 2:47 PM The Open Journals editorial robot < @.***> wrote:

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[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "doi" (NAME) [#<BibTeX::Bibliography data=[9]>, "@", #<BibTeX::Entry >, {:title=>["TDA: Statistical Tools for Topological Data Analysis"], :author=>["Brittany T. Fasy and Jisu Kim and Fabrizio Lecci and Clement Maria and David L. Millman and Vincent Rouvreau."], :year=>["2021"], :note=>["R package version 1.7.7"], :url=>["https://CRAN.R-project.org/package=TDA"]}]

[uislambekov]

@editorialbot generate pdf

On Thu, Aug 8, 2024 at 2:47 PM The Open Journals editorial robot < @.***> wrote:

Hello human, I'm @editorialbot https://github.com/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

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7092#issuecomment-2276448191, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASAV27FQ3QRGCI7FZRYM3EDZQO4KLAVCNFSM6AAAAABMHBWVWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZWGQ2DQMJZGE . You are receiving this because you were mentioned.Message ID: @.***>

[editorialbot]

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

[editorialbot]

Five most similar historical JOSS papers:

TDAstats: R pipeline for computing persistent homology in topological data analysis Submitting author: @rrrlw Handling editor: @leeper (Retired) Reviewers: @corybrunson Similarity score: 0.6905

Ripser.py: A Lean Persistent Homology Library for Python Submitting author: @sauln Handling editor: @arokem (Retired) Reviewers: @lmcinnes Similarity score: 0.6767

Ripserer.jl: flexible and efficient persistent homology computation in Julia Submitting author: @mtsch Handling editor: @VivianePons (Retired) Reviewers: @juliohm, @sauln Similarity score: 0.6621

DREiMac: Dimensionality Reduction with Eilenberg-MacLane Coordinates Submitting author: @LuisScoccola Handling editor: @fabian-s (Active) Reviewers: @mtsch, @raphaelreinauer Similarity score: 0.6434

Akmedoids R package for generating directionally-homogeneous clusters of longitudinal data sets Submitting author: @MAnalytics Handling editor: @karthik (Retired) Reviewers: @karthik, @njtierney Similarity score: 0.6429

⚠️ Note to editors: If these papers look like they might be a good match, click through to the review issue for that paper and invite one or more of the authors before considering asking the reviewers of these papers to review again for JOSS.

[uislambekov]

Thank you for your email. I have added the missing DOIs and reuploaded the .bib file. After running the @editorialbot generate command, Table 1 in the generated pdf file doesn't show the "check marks" found in the paper.md. When I preview paper.md as a pdf in RStudio, these check marks show up properly in Table 1. Please let me know if you would like me to try to fix it. Thank you!

On Thu, Aug 8, 2024 at 2:59 PM Daniel S. Katz @.***> wrote:

👋 @uislambekov https://github.com/uislambekov - Thanks for your submission.

Due to the relatively small amount of code, the editors will now discuss if it meets the substantial scholarly effort https://joss.readthedocs.io/en/latest/submitting.html#substantial-scholarly-effort criterion for review by JOSS. You should hear back in a week or so.

In addition, you could work on the possibly missing DOIs that editorialbot suggests, but note that some may be incorrect. Please feel free to make changes to your .bib file, then use the command @editorialbot check references to check again, and the command @editorialbot generate pdf when the references are right to make a new PDF. editorialbot commands need to be the first entry in a new comment.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7092#issuecomment-2276467988, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASAV27DW54M3IWDTSD26WODZQO5ZJAVCNFSM6AAAAABMHBWVWWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZWGQ3DOOJYHA . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

👋 @uislambekov - I'm sorry to say that after discussion amongst the JOSS editors, we have decided that this submission does not meet the substantial scholarly effort criterion for review by JOSS. Please see https://joss.readthedocs.io/en/latest/submitting.html#other-venues-for-reviewing-and-publishing-software-packages for other suggestions for how you might receive credit for your work.

[danielskatz]

@editorialbot reject

[editorialbot]

Paper rejected.