[PRE REVIEW]: corrp: An R package for multiple correlation-like analysis and clustering in mixed data

[editorialbot]

Submitting author: !--author-handle-->@PHS-Meantrix<!--end-author-handle-- (Paulo Henrique dos Santos) Repository: https://github.com/meantrix/corrp Branch with paper.md (empty if default branch): JOSS Version: 0.4.0 Editor: !--editor-->@jromanowska<!--end-editor-- Reviewers: @malcolmbarrett, @talegari Managing EiC: Chris Vernon

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/e99d49700a73e774a92a37abd9ccdaba"><img src="https://joss.theoj.org/papers/e99d49700a73e774a92a37abd9ccdaba/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/e99d49700a73e774a92a37abd9ccdaba/status.svg)](https://joss.theoj.org/papers/e99d49700a73e774a92a37abd9ccdaba)

Author instructions

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

@PHS-Meantrix 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.

Editor instructions

The JOSS submission bot @editorialbot is here to help you find and assign reviewers and start the main review. To find out what @editorialbot can do for you type:

@editorialbot commands

[editorialbot]

Hello human, 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]

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

✅ OK DOIs

- None

🟡 SKIP DOIs

- No DOI given, and none found for title: Notes on regression and inheritance in the case of...
- No DOI given, and none found for title: Detecting Novel Associations in Large Data Sets
- No DOI given, and none found for title: Precision-Recall-Gain Curves: PR Analysis Done Rig...
- No DOI given, and none found for title: Mathematical Methods of Statistics

❌ MISSING DOIs

- 10.1214/009053607000000505 may be a valid DOI for title: Measuring and testing independence by correlation ...
- 10.4324/9780203774441 may be a valid DOI for title: Applied Multiple Regression/Correlation Analysis f...
- 10.1016/0304-4076(75)90038-x may be a valid DOI for title: Statistical Decomposition Analysis: With Applicati...
- 10.1111/1467-9868.00293 may be a valid DOI for title: Estimating the number of clusters in a data set vi...

❌ INVALID DOIs

- None

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.90  T=0.02 s (1793.9 files/s, 198862.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               23            403            498           1171
Markdown                         4            204              0            722
C++                              4            162             52            489
TeX                              1              8              0             66
C/C++ Header                     2             14              7             60
YAML                             1              1              4             19
-------------------------------------------------------------------------------
SUM:                            35            792            561           2527
-------------------------------------------------------------------------------

Commit count by author:

   132  igor-siciliani
    20  paulo
     3  Igor-Siciliani

[editorialbot]

Paper file info:

📄 Wordcount for paper.md is 924

✅ The paper includes a Statement of need section

[editorialbot]

License info:

🟡 License found: GNU General Public License v3.0 (Check here for OSI approval)

[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:

latentcor: An R Package for estimating latent correlations from mixed data types Submitting author: @muellsen Handling editor: @crvernon (Active) Reviewers: @corybrunson, @rmflight Similarity score: 0.7228

Overlapping: a R package for Estimating Overlapping in Empirical Distributions Submitting author: @https://github.com/masspastore Handling editor: @arfon (Active) Reviewers: @soodoku, @russellpierce Similarity score: 0.6883

Philentropy: Information Theory and Distance Quantification with R Submitting author: @HajkD Handling editor: @leeper (Retired) Reviewers: @kellieotto Similarity score: 0.6872

Akmedoids R package for generating directionally-homogeneous clusters of longitudinal data sets Submitting author: @MAnalytics Handling editor: @karthik (Retired) Reviewers: @karthik, @njtierney Similarity score: 0.6711

TDApplied: An R package for machine learning and inference with persistence diagrams Submitting author: @shaelebrown Handling editor: @mahfuz05062 (Active) Reviewers: @EduPH, @peekxc Similarity score: 0.6691

⚠️ 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.

[crvernon]

@editorialbot query scope

:wave: @PHS-Meantrix - thanks for your submission to JOSS. I am going to run this one by our larger editorial board due to it's smaller code base to ensure it meets our substantial scholarly effort requirement. This should take about two weeks at the most. I'll let you know what I hear back ASAP.

[editorialbot]

Submission flagged for editorial review.

[PHS-Meantrix]

Dear JOSS Editorial Team,

Since it was our first submission, I initially thought there would be another step to review the PDF before finalizing the submission, but there wasn't one. After learning how to review the PDF and checking it, we’ve noticed that some tables need formatting, along with minor text updates and corrections to the DOIs in the references. We recently committed updates to the paper.md. How can we proceed with updating the submission?

Best regards, Paulo

Em sex., 30 de ago. de 2024 às 09:34, The Open Journals editorial robot < @.***> escreveu:

Submission flagged for editorial review.

— Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/7143#issuecomment-2321098578, or unsubscribe https://github.com/notifications/unsubscribe-auth/AXEKJLVOMHBEBD2LQITKAGLZUBRFBAVCNFSM6AAAAABNEFNURCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMRRGA4TQNJXHA . You are receiving this because you were mentioned.Message ID: @.***>

-- Atenciosamente, Paulo H. dos Santos

[danielskatz]

@PHS-Meantrix - you can freely edit the submission, at least before the review starts.

Also, bot commands you can use are @editorialbot check references (to check the references/DOIs), and @editorialbot generate pdf (to make a new PDF). editorialbot commands need to be the first entry in a new comment.

[PHS-Meantrix]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1098/rspl.1895.0041 is OK
- 10.1214/009053607000000505 is OK
- 10.1126/science.1205438 is OK
- 10.5281/ZENODO.4091345 is OK
- 10.4324/9780203774441 is OK
- 10.1515/9781400883868 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1016/C2013-0-07379-0 is INVALID
- https://doi.org/10.1016/j.jbi.2010.02.001 is INVALID because of 'https://doi.org/' prefix

[PHS-Meantrix]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1098/rspl.1895.0041 is OK
- 10.1214/009053607000000505 is OK
- 10.1126/science.1205438 is OK
- 10.5281/ZENODO.4091345 is OK
- 10.4324/9780203774441 is OK
- 10.1515/9781400883868 is OK
- 10.1016/j.jbi.2010.02.001 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- None

❌ INVALID DOIs

- 10.1016/C2013-0-07379-0 is INVALID

[PHS-Meantrix]

@editorialbot check references

[editorialbot]

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

✅ OK DOIs

- 10.1098/rspl.1895.0041 is OK
- 10.1214/009053607000000505 is OK
- 10.1126/science.1205438 is OK
- 10.5281/ZENODO.4091345 is OK
- 10.4324/9780203774441 is OK
- 10.1515/9781400883868 is OK
- 10.1016/j.jbi.2010.02.001 is OK

🟡 SKIP DOIs

- None

❌ MISSING DOIs

- 10.1016/0304-4076(75)90038-x may be a valid DOI for title: Statistical Decomposition Analysis: With Applicati...

❌ INVALID DOIs

- None

[PHS-Meantrix]

@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:

[PHS-Meantrix]

@danielskatz Thanks, another thing we want to know how to change the citation format for our author names. Instead of "Siciliani, & dos Santos," can we change to Igor D.S. Siciliani, & P.H. Santos?

Also, there is no doi for Henri Theil's book. How to proceed with this?

[editorialbot]

Five most similar historical JOSS papers:

latentcor: An R Package for estimating latent correlations from mixed data types Submitting author: @muellsen Handling editor: @crvernon (Active) Reviewers: @corybrunson, @rmflight Similarity score: 0.7221

partition: A fast and flexible framework for data reduction in R Submitting author: @malcolmbarrett Handling editor: @csoneson (Active) Reviewers: @lmweber, @clauswilke Similarity score: 0.7080

Akmedoids R package for generating directionally-homogeneous clusters of longitudinal data sets Submitting author: @MAnalytics Handling editor: @karthik (Retired) Reviewers: @karthik, @njtierney Similarity score: 0.7073

scPCA: A toolbox for sparse contrastive principal component analysis in R Submitting author: @PhilBoileau Handling editor: @csoneson (Active) Reviewers: @fabian-s, @LTLA Similarity score: 0.7030

visxhclust: An R Shiny package for visual exploration of hierarchical clustering Submitting author: @rhenkin Handling editor: @osorensen (Active) Reviewers: @jonjoncardoso, @wiljnich Similarity score: 0.7010

⚠️ 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]

The citation format can't be changed, unless there is something incorrect in the parsing of your names, which doesn't appear to be the case here.

And for items with no DOI, that's fine - you don't need to do anything.

[crvernon]

:wave: @PHS-Meantrix - I am pleased to inform you that our larger editorial board has supported this moving into review. I will now try to get you a topic editor assigned. Thank you for your patience.

[crvernon]

@editorialbot invite @jromanowska as editor

:wave: @jromanowska - can you take this one on as editor?

[editorialbot]

Invitation to edit this submission sent!

[jromanowska]

@crvernon I can! :)

@editorialbot assign me as editor

[jromanowska]

@editorialbot assign me as editor

[editorialbot]

Assigned! @jromanowska is now the editor

[jromanowska]

Hi, @PHS-Meantrix :wave: I will take care of the process from now on. I will try to find reviewers, but please let me know if you have any suggestions (or oppositions). When naming reviewers who have GitHub accounts, write their GitHub handles without @, so that they won't get notified.

[jromanowska]

@PHS-Meantrix , before I start, I have one question. In the acknowledgments you write that you took inspiration for the package from the code written by Srikanth Komala Sheshachala. Could you specify if there are any parts of the code that are copied from there? I can't see any licence in their repo (https://github.com/talegari/sidekicks/), so if you have used their code, we should probably invite them as co-author.

[PHS-Meantrix]

@jromanowska No part of the code was utilized. It was seen by @igor-siciliani, and he used just the idea of the function https://github.com/talegari/sidekicks/blob/master/R/cor2.R as inspiration for the mix of correlations.

[jromanowska]

I will try to find reviewers for your submission, @PHS-Meantrix . Let me know if you have any suggestions (or oppositions). When naming reviewers who have GitHub accounts, write their GitHub handles without @, so that they won't get notified.

[jromanowska]

:wave: @muellsen, @malcolmbarrett, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[malcolmbarrett]

I'm gearing up for a work trip and won't be available for about three weeks, but if that timeline is okay with you, I can review it.

[jromanowska]

@malcolmbarrett - thanks for the quick response! I think we can wait three weeks, I have not found the second reviewer yet, so it will anyway take time before the "real" review process starts. If you know that you can work on the review when you're back from the trip, it would be great to have you as a reviewer :)

[malcolmbarrett]

That shouldn't be a problem. Happy to do it then.

[jromanowska]

@editorialbot add @malcolmbarrett as reviewer

[editorialbot]

@malcolmbarrett added to the reviewers list!

[jromanowska]

:wave: @PhilBoileau & @talegari, would any of you be willing to review this submission for JOSS? We carry out our checklist-driven reviews here in GitHub issues and follow these guidelines: https://joss.readthedocs.io/en/latest/review_criteria.html

[talegari]

@jromanowska I can do this.

[jromanowska]

@editorialbot add @talegari as reviewer

[editorialbot]

@talegari added to the reviewers list!

[jromanowska]

@talegari , I will wait a couple more days before starting the actual review process, in case the other people I've pinged answer.

[jromanowska]

@editorialbot start review

[editorialbot]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/7319.