[PRE REVIEW]: cca-zoo

[whedon]

Submitting author: @jameschapman19 (James Chapman) Repository: https://github.com/jameschapman19/cca_zoo Version: v.1.9.0 Editor: @emdupre Reviewers: @robbisg, @hugorichard, @ejolly Managing EiC: Kyle Niemeyer

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

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Author instructions

Thanks for submitting your paper to JOSS @jameschapman19. Currently, there isn't an JOSS editor assigned to your paper.

The author's suggestion for the handling editor is @emdupre.

@jameschapman19 if you have any suggestions for potential reviewers then please mention them here in this thread (without tagging them with an @). In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission (please start at the bottom of the list).

Editor instructions

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

@whedon commands

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

For a list of things I can do to help you, just type:

@whedon commands

For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

@whedon generate pdf

[whedon]

Wordcount for paper.md is 1397

[whedon]

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.47 s (132.8 files/s, 24730.3 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          36            779           1686           4621
Jupyter Notebook                 3              0           1343           1814
reStructuredText                14            216            139            255
TeX                              1             26              0            225
Markdown                         2             47              0            216
YAML                             4             17             17             91
DOS Batch                        1              8              1             26
make                             1              4              7              9
-------------------------------------------------------------------------------
SUM:                            62           1097           3193           7257
-------------------------------------------------------------------------------

Statistical information for the repository '275a48e57ebcfa289b57abfc' was
gathered on 2021/10/07.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Hao-Ting Wang                    2            82             25            0.20
James Chapman                  423         17935          13864           58.33
jameschapman                    55         12783           9824           41.47

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Hao-Ting Wang                48           58.5          4.1                6.25
James Chapman              7038           39.2          2.5                7.22

[whedon]

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

OK DOIs

- None

MISSING DOIs

- 10.2307/2333955 may be a valid DOI for title: Relations between two sets of variates
- 10.1016/0304-4076(76)90010-5 may be a valid DOI for title: Canonical ridge and econometrics of joint production
- 10.1162/0899766042321814 may be a valid DOI for title: Canonical correlation analysis: An overview with application to learning methods
- 10.1007/s11336-011-9206-8 may be a valid DOI for title: Regularized generalized canonical correlation analysis
- 10.1093/biostatistics/kxp008 may be a valid DOI for title: A penalized matrix decomposition, with applications to sparse principal components and canonical correlation analysis
- 10.2202/1544-6115.1329 may be a valid DOI for title: Quantifying the association between gene expressions and DNA-markers by penalized canonical correlation analysis
- 10.2202/1544-6115.1406 may be a valid DOI for title: Sparse canonical correlation analysis with application to genomic data integration
- 10.1111/biom.13043 may be a valid DOI for title: An iterative penalized least squares approach to sparse canonical correlation analysis
- 10.3389/fninf.2016.00049 may be a valid DOI for title: Pyrcca: regularized kernel canonical correlation analysis in python and its applications to neuroimaging
- 10.1007/978-1-4612-4228-4_3 may be a valid DOI for title: The canonical correlations of matrix pairs and their numerical computation
- 10.1109/allerton.2015.7447071 may be a valid DOI for title: Stochastic optimization for deep CCA via nonlinear orthogonal iterations
- 10.1109/cvpr.2007.383137 may be a valid DOI for title: Tensor canonical correlation analysis for action classification
- 10.1109/tnn.2007.891186 may be a valid DOI for title: Variational Bayesian approach to canonical correlation analysis

INVALID DOIs

- None

[whedon]

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

[kyleniemeyer]

Hi @emdupre, could you edit this submission?

[kyleniemeyer]

@whedon invite @emdupre as editor

[whedon]

@emdupre has been invited to edit this submission.

[emdupre]

Thank you for the invitation, @kyleniemeyer !

I just wanted to note that I have an ongoing collaboration with one of the author's (HTW) current affiliations. We have never directly worked together, though, and I am confident that I can act as an impartial editor on the submission. If it's OK with you to note and waive the conflict, I'm happy to edit this submission !

[kyleniemeyer]

@emdupre yes, I think that is fine—thanks for the heads up though!

[emdupre]

@whedon assign @emdupre as editor

[whedon]

OK, the editor is @emdupre

[emdupre]

:wave: Hi @jameschapman19, and thank you for your submission to JOSS !

If you have any suggestions for potential reviewers, please let me know by listing their names or GitHub handles (without the @, so they don't receive a notification) here.

[jameschapman19]

Hi @emdupre - new to the process here so do you mean scroll through the same list where I found you during submission? Or could they be anyone?

[emdupre]

You can suggest reviewers from any relevant project, though we often recommend starting with this list of people as they have already agreed to review for JOSS (please start at the bottom of the list).

[jameschapman19]

Got it - picked out a few names from the bottom with some interests that overlap the software (also spied my own name after recently volunteering!)

kmichael08 ("Machine Learning Interpretable Machine Learning Natural Language Processing Statistics")

GeekLogan ("Neuroscience Neuroinformatics Data Science Bioinformatics Genomics")

joewandy (metabolomics, bioinformatics, omics integration, machine learning)

robbisg ("Neuroimaging Neuroscience Machine Learning")

[jameschapman19]

not sure how many you need - could keep going if they don't respond!

[emdupre]

Thanks, @jameschapman19 ! This is helpful :slightly_smiling_face:

I'll pull together a list of folks to reach out to as reviewers based on this and my own recommendations. I'll update this thread with that outreach.

[emdupre]

Hi @kmichael08 @robbisg @ejolly @saigerutherford @hugorichard @mnarayan :wave:

Would you be willing to review cca-zoo: a python package for implementing models from the canonical correlation analysis family for JOSS (the Journal of Open Source Software) ?

The review takes place on GitHub and focuses on the software and this short paper: https://github.com/openjournals/joss-papers/blob/joss.03806/joss.03806/10.21105.joss.03806.pdf

If you're available to review this work, please let me know and I'll add you as a reviewer. Once I have sufficient reviewers I'll open a dedicated review issue.

Thanks !

[robbisg]

Hi @emdupre :wave:

Cool package! I can review it!

[hugorichard]

Hi @emdupre ! I can review this package !

[ejolly]

Hey @emdupre!! I'm happy to review too!

[emdupre]

Thank you, @robbisg @hugorichard @ejolly !!! I'll add you as reviewers for this submission and we can get the process started :rocket:

.@kmichael08 @saigerutherford @mnarayan, we now have enough reviewers for this submission, but I may contact you again for future reviews if that's ok with you ! Thank you for your consideration :sunflower:

[emdupre]

@whedon add @robbisg as reviewer

[whedon]

OK, @robbisg is now a reviewer

[emdupre]

@whedon add @hugorichard as reviewer

[whedon]

OK, @hugorichard is now a reviewer

[emdupre]

@whedon add @ejolly as reviewer

[whedon]

OK, @ejolly is now a reviewer

[emdupre]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/3823.