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[PRE REVIEW]: corrp: An R package for multiple correlation-like analysis and clustering in mixed data #7143

Open editorialbot opened 2 weeks ago

editorialbot commented 2 weeks ago

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: Pending Managing EiC: Chris Vernon

Status

status

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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 commented 2 weeks ago

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 commented 2 weeks ago 
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 commented 2 weeks ago

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 commented 2 weeks ago

Paper file info:

📄 Wordcount for paper.md is 924

✅ The paper includes a Statement of need section

editorialbot commented 2 weeks ago

License info:

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

editorialbot commented 2 weeks ago

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

editorialbot commented 2 weeks ago

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 commented 2 weeks ago

@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 commented 2 weeks ago

Submission flagged for editorial review.

PHS-Meantrix commented 2 weeks ago

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 commented 1 week ago

@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 commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
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 commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
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 commented 1 week ago

@editorialbot check references

editorialbot commented 1 week ago 
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 commented 1 week ago

@editorialbot generate pdf

editorialbot commented 1 week ago

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

PHS-Meantrix commented 1 week ago

@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 commented 1 week ago

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 commented 1 week ago

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 commented 6 days ago

: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 commented 6 days ago

@editorialbot invite @jromanowska as editor

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

editorialbot commented 6 days ago

Invitation to edit this submission sent!

jromanowska commented 5 days ago

@crvernon I can! :)

@editorialbot assign me as editor

jromanowska commented 5 days ago

@editorialbot assign me as editor

editorialbot commented 5 days ago

Assigned! @jromanowska is now the editor

jromanowska commented 5 days ago

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 commented 5 days ago

@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 commented 5 days ago

@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 commented 4 days ago

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.