[PRE 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: v3.0.2 Editor: !--editor-->@mahfuz05062<!--end-editor-- Reviewers: @EduPH, @peekxc Managing EiC: Daniel S. Katz

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Thanks for submitting your paper to JOSS @shaelebrown. Currently, there isn't a JOSS editor assigned to your paper.

@shaelebrown if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission.

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[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.09 s (840.6 files/s, 253103.2 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               32            980           2907           4283
C++                             17            809           2297           4256
C/C++ Header                    16            487           2160           1611
Rmd                              6            536            820            868
TeX                              1            107              0            757
Markdown                         4             73              0            208
YAML                             1              3              4             18
-------------------------------------------------------------------------------
SUM:                            77           2995           8188          12001
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 578

[editorialbot]

Failed to discover a valid open source 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:

Ripser.py: A Lean Persistent Homology Library for Python Submitting author: @sauln Handling editor: @arokem (Retired) Reviewers: @lmcinnes Similarity score: 0.8428

giotto-deep: A Python Package for Topological Deep Learning Submitting author: @matteocao Handling editor: @osorensen (Active) Reviewers: @EduPH, @leotrs, @ismailguzel Similarity score: 0.8342

Kepler Mapper: A flexible Python implementation of the Mapper algorithm. Submitting author: @sauln Handling editor: @leouieda (Retired) Reviewers: @ixjlyons, @lmcinnes Similarity score: 0.8316

PRDA: An R package for Prospective and Retrospective Design Analysis Submitting author: @ClaudioZandonella Handling editor: @cMadan (Active) Reviewers: @DominiqueMakowski, @mmrabe Similarity score: 0.8183

tidyLPA: An R Package to Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software Submitting author: @jrosen48 Handling editor: @arfon (Active) Reviewers: @jnese, @strengejacke Similarity score: 0.8123

⚠️ 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]

👋 @shaelebrown - thanks for your submission. You'll need to license it with an OSI-approved license before we can proceed. I also wonder if you might want to add any graphics to your paper to make the work more clear to those outside the field?

[danielskatz]

@editorialbot check references

[editorialbot]

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

OK DOIs

- 10.18637/jss.v014.i12 is OK
- 10.5281/zenodo.2533369 is OK
- 10.21105/joss.00860 is OK
- 10.1007/978-3-540-33259-6_7 is OK
- 10.1145/2939672.2939785 is OK
- 10.3389/frai.2021.681108 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1371/journal.pone.0255859 is OK
- 10.3389/fphy.2021.572216 is OK
- 10.18637/jss.v040.i08 is OK
- 10.3389/fnsys.2013.00101 is OK
- 10.1101/2021.08.05.455149 is OK
- 10.3390/brainsci9060144 is OK
- 10.1162/netn_a_00073 is OK
- 10.1007/978-3-319-10443-0_38 is OK
- 10.1152/jn.00338.2011 is OK
- 10.3389/neuro.06.004.2008 is OK
- 10.1145/1810959.1811004 is OK
- 10.3389/frai.2021.667963 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1109/ISBI.2011.5872535 is OK
- 10.1038/nn.4135 is OK
- 10.1145/3064175 is OK
- 10.1007/978-3-540-33037-0_14 is OK
- 10.32614/RJ-2021-033 is OK
- 10.1162/netn_a_00095 is OK
- 10.3389/fncom.2021.616748 is OK
- 10.1007/s10827-016-0608-6 is OK

MISSING DOIs

- 10.1093/oso/9780198522294.002.0003 may be a valid DOI for title: Statistical methods for research workers.
- 10.1007/s00454-014-9604-7 may be a valid DOI for title: Frechet Means for Distributions of Persistence Diagrams
- 10.1109/sfcs.2000.892133 may be a valid DOI for title: Topological Persistence and Simplification
- 10.1109/cvpr.2015.7299106 may be a valid DOI for title: A Stable Multi-Scale Kernel for Topological Machine Learning
- 10.1016/j.neuroimage.2016.09.008 may be a valid DOI for title: Noise contributions to the fMRI signal: An overview
- 10.1038/s41593-018-0312-0 may be a valid DOI for title: Human cognition involves the dynamic integration of neural activity and neuromodulatory systems
- 10.1007/978-3-030-00755-3_8 may be a valid DOI for title: Topological Data Analysis of Functional MRI Connectivity in Time and Space Domains
- 10.1523/eneuro.0543-19.2020 may be a valid DOI for title: Topological Data Analysis reveals robust alterations in the whole-brain and frontal lobe functional connectomes in Attention-Deficit/Hyperactivity Disorder
- 10.1007/s11263-007-0056-x may be a valid DOI for title: On the Local Behavior of Spaces of Natural Images
- 10.32614/rj-2011-002 may be a valid DOI for title: testthat: Get Started with Testing
- 10.1038/s41598-021-88027-8 may be a valid DOI for title: Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks
- 10.1162/089976698300017467 may be a valid DOI for title: Nonlinear Component Analysis as a Kernel Eigenvalue Problem
- 10.1201/9781420011036-7 may be a valid DOI for title: Statistical Inference
- 10.1145/1542362.1542406 may be a valid DOI for title: Persistent Cohomology and Circular Coordinates
- 10.1088/0266-5611/27/12/124003 may be a valid DOI for title: Dualities in persistent (co)homology
- 10.1214/14-aos1252 may be a valid DOI for title: Confidence Sets for Persistence Diagrams
- 10.1186/s13244-023-01413-w may be a valid DOI for title: Topological data analysis in medical imaging: current state of the art
- 10.1038/s41467-018-03664-4 may be a valid DOI for title: Towards a new approach to reveal dynamical organization of the brain using topological data analysis

INVALID DOIs

- https://doi.org/10.1016/j.jsc.2016.03.009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2016.12.018 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cub.2017.05.010 is INVALID because of 'https://doi.org/' prefix

[danielskatz]

👋 @shaelebrown - in addition, @editorialbot checks all references in the references file. Since many of yours are not actually cited in the paper, you might want to make a paper.bib file that just contains the ones you need, and use that in the paper.

Either way, you will have to fix some DOIs, as shown in the result of the @editorialbot check references command, 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 (or if you change the .md file, eg. by adding a figure) to make a new PDF. editorialbot commands need to be the first entry in a new comment.

When you are ready to proceed (no correct missing or invalid DOIs, an open source license, perhaps a figure in the paper), please ping me.

[editorialbot]

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

OK DOIs

- 10.18637/jss.v014.i12 is OK
- 10.5281/zenodo.2533369 is OK
- 10.21105/joss.00860 is OK
- 10.1007/978-3-540-33259-6_7 is OK
- 10.1145/2939672.2939785 is OK
- 10.3389/frai.2021.681108 is OK
- 10.1007/s00454-004-1146-y is OK
- 10.1371/journal.pone.0255859 is OK
- 10.3389/fphy.2021.572216 is OK
- 10.18637/jss.v040.i08 is OK
- 10.3389/fnsys.2013.00101 is OK
- 10.1101/2021.08.05.455149 is OK
- 10.3390/brainsci9060144 is OK
- 10.1162/netn_a_00073 is OK
- 10.1007/978-3-319-10443-0_38 is OK
- 10.1152/jn.00338.2011 is OK
- 10.3389/neuro.06.004.2008 is OK
- 10.1145/1810959.1811004 is OK
- 10.3389/frai.2021.667963 is OK
- 10.18653/v1/2022.repl4nlp-1.18 is OK
- 10.1109/ISBI.2011.5872535 is OK
- 10.1038/nn.4135 is OK
- 10.1145/3064175 is OK
- 10.1007/978-3-540-33037-0_14 is OK
- 10.32614/RJ-2021-033 is OK
- 10.1162/netn_a_00095 is OK
- 10.3389/fncom.2021.616748 is OK
- 10.1007/s10827-016-0608-6 is OK

MISSING DOIs

- 10.1093/oso/9780198522294.002.0003 may be a valid DOI for title: Statistical methods for research workers.
- 10.1007/s00454-014-9604-7 may be a valid DOI for title: Frechet Means for Distributions of Persistence Diagrams
- 10.1109/sfcs.2000.892133 may be a valid DOI for title: Topological Persistence and Simplification
- 10.1109/cvpr.2015.7299106 may be a valid DOI for title: A Stable Multi-Scale Kernel for Topological Machine Learning
- 10.1016/j.neuroimage.2016.09.008 may be a valid DOI for title: Noise contributions to the fMRI signal: An overview
- 10.1038/s41593-018-0312-0 may be a valid DOI for title: Human cognition involves the dynamic integration of neural activity and neuromodulatory systems
- 10.1007/978-3-030-00755-3_8 may be a valid DOI for title: Topological Data Analysis of Functional MRI Connectivity in Time and Space Domains
- 10.1523/eneuro.0543-19.2020 may be a valid DOI for title: Topological Data Analysis reveals robust alterations in the whole-brain and frontal lobe functional connectomes in Attention-Deficit/Hyperactivity Disorder
- 10.1007/s11263-007-0056-x may be a valid DOI for title: On the Local Behavior of Spaces of Natural Images
- 10.32614/rj-2011-002 may be a valid DOI for title: testthat: Get Started with Testing
- 10.1038/s41598-021-88027-8 may be a valid DOI for title: Machine learning with persistent homology and chemical word embeddings improves prediction accuracy and interpretability in metal-organic frameworks
- 10.1162/089976698300017467 may be a valid DOI for title: Nonlinear Component Analysis as a Kernel Eigenvalue Problem
- 10.1201/9781420011036-7 may be a valid DOI for title: Statistical Inference
- 10.1145/1542362.1542406 may be a valid DOI for title: Persistent Cohomology and Circular Coordinates
- 10.1088/0266-5611/27/12/124003 may be a valid DOI for title: Dualities in persistent (co)homology
- 10.1214/14-aos1252 may be a valid DOI for title: Confidence Sets for Persistence Diagrams
- 10.1186/s13244-023-01413-w may be a valid DOI for title: Topological data analysis in medical imaging: current state of the art
- 10.1038/s41467-018-03664-4 may be a valid DOI for title: Towards a new approach to reveal dynamical organization of the brain using topological data analysis

INVALID DOIs

- https://doi.org/10.1016/j.jsc.2016.03.009 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.neuroimage.2016.12.018 is INVALID because of 'https://doi.org/' prefix
- https://doi.org/10.1016/j.cub.2017.05.010 is INVALID because of 'https://doi.org/' prefix

[shaelebrown]

Hi Daniel,

Thanks for that! I thought that GPL3 would be covered but I can see that it is not. Do I need to change the license on just my github repo or submit a package update to CRAN with the new license? Looking to add a graphic now..

On Thu, Jan 25, 2024 at 3:00 PM Daniel S. Katz @.***> wrote:

👋 @shaelebrown https://github.com/shaelebrown - thanks for your submission. You'll need to license it with an OSI-approved license before we can proceed. I also wonder if you might want to add any graphics to your paper to make the work more clear to those outside the field?

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6283#issuecomment-1910901074, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANP6DQU3UXD2IJGWHV4SBN3YQK2UXAVCNFSM6AAAAABCLCWV3SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJQHEYDCMBXGQ . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

using GPL3 is fine, but I didn't see it in the repo. Now I see it in the DESCRIPTION file. You could also add a license file (see https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository) to make GitHub recognize the license, but it's not technically needed for JOSS.

[shaelebrown]

@editorialbot check references @editorialbot generate pdf

[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

[shaelebrown]

@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:

[editorialbot]

Five most similar historical JOSS papers:

Ripser.py: A Lean Persistent Homology Library for Python Submitting author: @sauln Handling editor: @arokem (Retired) Reviewers: @lmcinnes Similarity score: 0.8474

Kepler Mapper: A flexible Python implementation of the Mapper algorithm. Submitting author: @sauln Handling editor: @leouieda (Retired) Reviewers: @ixjlyons, @lmcinnes Similarity score: 0.8340

giotto-deep: A Python Package for Topological Deep Learning Submitting author: @matteocao Handling editor: @osorensen (Active) Reviewers: @EduPH, @leotrs, @ismailguzel Similarity score: 0.8329

Persistable: persistent and stable clustering Submitting author: @LuisScoccola Handling editor: @rkurchin (Active) Reviewers: @lmcinnes, @AP6YC Similarity score: 0.8147

PRDA: An R package for Prospective and Retrospective Design Analysis Submitting author: @ClaudioZandonella Handling editor: @cMadan (Active) Reviewers: @DominiqueMakowski, @mmrabe Similarity score: 0.8146

⚠️ 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.

[shaelebrown]

Thanks Daniel. I've added a license file to the JOSS branch (not the main branch) to ease with the review, fixed and checked the bibliography and added a figure. Please let me know if all looks good and we can proceed, thanks!

On Fri, Jan 26, 2024 at 11:01 AM Daniel S. Katz @.***> wrote:

using GPL3 is fine, but I didn't see it in the repo. Now I see it in the DESCRIPTION file. You could also add a license file (see https://docs.github.com/en/communities/setting-up-your-project-for-healthy-contributions/adding-a-license-to-a-repository) to make GitHub recognize the license, but it's not technically needed for JOSS.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6283#issuecomment-1912299605, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANP6DQXWH2NN3IU3OKTR3U3YQPHMBAVCNFSM6AAAAABCLCWV3SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJSGI4TSNRQGU . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

@editorialbot check repository

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=0.10 s (752.8 files/s, 228017.6 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

[danielskatz]

@shaelebrown - thanks, this all looks good. I'll proceed to looking for an editor. While I do so, if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission, or make suggestions from outside this list.

[danielskatz]

👋 @xuanxu, @vissarion, @drvinceknight, @olexandr-konovalov - I know you are all at your marked maximum editing loads currently, but in case one of you is close to finishing up one, or could take on an extra editing assignment, please let me know.

[danielskatz]

👋 @mahfuz05062 - As a new JOSS editor, would this submission be of interest to you as your first?

[mahfuz05062]

@danielskatz Sure. I don't have experience with persistence diagrams, but I have good experience with R and some experience with MDS so I should be good.

[danielskatz]

Thanks very much @mahfuz05062 - I'll assign you as editor and let you get started. Please let me know if you need any help, either here or via slack if that's easier.

[danielskatz]

@editorialbot assign @mahfuz05062 as editor

[editorialbot]

Assigned! @mahfuz05062 is now the editor

[shaelebrown]

Wonderful! @mahfuz05062 I look forward to hearing your input. Daniel I can see that @EduPH has expertise in R and topological data analysis (the other members of the list with similar credentials I have collaborated with, rrrlw and corybrunson). Some other options would be the contributor of the R package TDA Jisu Kim (https://jkim82133.github.io/research.html), the creator of the Ball mapper algorithm and R package Pawel Dlotko ( https://dioscuri-tda.org/members/pawel.html), an author of several TDA R software packages Matt Pieckenbrock (https://peekxc.github.io), but I'm open to others. If @lmcinnes or @sauln are open to coming to the dark side of R then they would also be good options.

On Sun, Jan 28, 2024 at 12:42 PM Daniel S. Katz @.***> wrote:

@shaelebrown https://github.com/shaelebrown - thanks, this all looks good. I'll proceed to looking for an editor. While I do so, if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people https://reviewers.joss.theoj.org/lookup that have already agreed to review and may be suitable for this submission, or make suggestions from outside this list.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6283#issuecomment-1913671484, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANP6DQQZLFGRHPTBQ7JYFSLYQ2EX7AVCNFSM6AAAAABCLCWV3SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTGY3TCNBYGQ . You are receiving this because you were mentioned.Message ID: @.***>

[danielskatz]

@shaelebrown - just a reminder, please don't tag potential reviewers - we don't need to add notifications to anyone until the editor decides on who to invite...

@shaelebrown - thanks, this all looks good. I'll proceed to looking for an editor. While I do so, if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people that have already agreed to review and may be suitable for this submission, or make suggestions from outside this list.

[shaelebrown]

So sorry about that, will make sure to avoid this going forward.

On Sun, Jan 28, 2024 at 2:40 PM Daniel S. Katz @.***> wrote:

@shaelebrown https://github.com/shaelebrown - just a reminder, please don't tag potential reviewers - we don't need to add notifications to anyone until the editor decides on who to invite...

@shaelebrown https://github.com/shaelebrown - thanks, this all looks good. I'll proceed to looking for an editor. While I do so, if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). You can search the list of people https://reviewers.joss.theoj.org/lookup that have already agreed to review and may be suitable for this submission, or make suggestions from outside this list.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/6283#issuecomment-1913700873, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANP6DQRK2K6GRHKRUPWI3LDYQ2STRAVCNFSM6AAAAABCLCWV3SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJTG4YDAOBXGM . You are receiving this because you were mentioned.Message ID: @.***>

[mahfuz05062]

Hi @EduPH, do you have time and are you willing to review this submission? I am reaching out to some of the potential reviewers not in the JOSS network and will keep everyone updated about that.

[mahfuz05062]

As an update, I sent emails to Jisu Kim, Pawel Dlotko, and Matt Pieckenbrock on Tuesday and waiting for a reply. I will send a follow-up email tomorrow but if it doesn't work out, I will look into both the remaining options and additional potential reviewers. Thank you for your patience as we find out reviewers.

[EduPH]

Hi @mahfuz05062. Sorry for my late reply, I can review this submission.

[mahfuz05062]

Thank you @EduPH for agreeing to review this submission! Once I find another reviewer, we can start the review process.

[mahfuz05062]

Update from my side: Matt Pieckenbrock has agreed (as a reply to my email) to review the paper. Once he joins JOSS, I will officially invite him here.

[mahfuz05062]

Hi @peekxc, welcome to JOSS! Thank you for agreeing to review this submission over email. Please confirm again here for visibility.

[peekxc]

Hi @peekxc, welcome to JOSS! Thank you for agreeing to review this submission over email. Please confirm again here for visibility.

Confirmed

[mahfuz05062]

@editorialbot add @EduPH as reviewer

[editorialbot]

@EduPH added to the reviewers list!

[mahfuz05062]

@editorialbot add @peekxc as reviewer

[editorialbot]

@peekxc added to the reviewers list!

[mahfuz05062]

@danielskatz We have two reviewers ready to review this paper. Is there anything else we need before we start the review process?

[danielskatz]

No, nothing more.

[mahfuz05062]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/6321.