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[REVIEW]: dcTensor: An R package for discrete matrix/tensor decomposition #5664

Closed editorialbot closed 10 months ago

editorialbot commented 11 months ago

Submitting author: !--author-handle-->@kokitsuyuzaki<!--end-author-handle-- (Koki Tsuyuzaki) Repository: https://github.com/rikenbit/dcTensor Branch with paper.md (empty if default branch): Version: v1.2.3 Editor: !--editor-->@diehlpk<!--end-editor-- Reviewers: @dekuenstle, @CeciliaCoelho Archive: 10.5281/zenodo.8275544

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Markdown: [![status](https://joss.theoj.org/papers/41a68242a41f762bd768ff44fc3b6b97/status.svg)](https://joss.theoj.org/papers/41a68242a41f762bd768ff44fc3b6b97)

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editorialbot commented 11 months ago

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editorialbot commented 11 months ago 
Software report:

github.com/AlDanial/cloc v 1.88  T=0.03 s (2398.1 files/s, 189715.9 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               46            289            266           2983
Rmd                              7            226            432            265
Markdown                         6             60              0            203
TeX                              2             23             21            140
YAML                             1             11             13             45
Dockerfile                       1              1              2              4
-------------------------------------------------------------------------------
SUM:                            63            610            734           3640
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository
editorialbot commented 11 months ago

Wordcount for paper.md is 567

editorialbot commented 11 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- None

MISSING DOIs

- 10.1109/icdm.2007.99 may be a valid DOI for title: Binary Matrix Factorization with Applications
- 10.1109/icassp.2007.367106 may be a valid DOI for title: Non-negative Tensor Factorization using Alpha and Beta Divergence
- 10.1109/cvpr.2007.383405 may be a valid DOI for title: Nonnegative Tucker Decomposition
- 10.1038/44565 may be a valid DOI for title: Learning the parts of objects by non-negative matrix factorization
- 10.1186/s13059-019-1900-3 may be a valid DOI for title: Benchmarking principal component analysis for large-scale single-cell RNA-sequencing
- 10.1142/9789812776136_0027 may be a valid DOI for title: Extracting Gene Expression Profiles Common to Colon and Pancreatic Adenocarcinoma using Simultaneous nonnegative matrix factorization
- 10.1093/nar/gks725 may be a valid DOI for title: Discovery of multi-dimensional modules by integrative analysis of cancer genomic data
- 10.1007/978-3-642-15995-4_43 may be a valid DOI for title: Probabilistic Latent Tensor Factorization
- 10.1093/bioinformatics/btv544 may be a valid DOI for title: A non-negative matrix factorization method for detecting modules in heterogeneous omics multi-modal data

INVALID DOIs

- None
editorialbot commented 11 months ago

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

dekuenstle commented 11 months ago

Review checklist for @dekuenstle

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

CeciliaCoelho commented 11 months ago

Review checklist for @CeciliaCoelho

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

dekuenstle commented 11 months ago

The submission presents a highly specialized R package for discrete matrix decomposition algorithms. The package is openly available (MIT-Licence on Github) and distributed according to R-standards on CRAN; the API is simple, and extensive unit tests are available (while it is unclear if they run automatically). However, I have some suggestions for improvement concerning the documentation and the manuscript.

The CRAN documentation provides a good explanation of the input parameters and expected data format as well as references to publications describing the implemented algorithms. Here it would be helpful to have a small summary of the algorithm in the Description field of each function, i.e. describing for what purpose the algorithm is used or how it is different from the others. The only installation instructions on the repository readme are aimed more at developers than end users because they install from Github instead of CRAN. The readme could be a good place to give users and developers separate instructions and add the missing community guidelines. The file LICENSE.md contains an MIT license statement; however, there is another file, LICENSE, with just a header that might be removed. Unit tests are available in the repository, but test coverage and automation are not documented. The Github action workflow "build_test_push.yml", running on push and pull, apparently is not running the test suite–––Test automation should be added or, if already done, documented.

The paper Summary provides a high-level introduction to discrete matrix decomposition. The arguments could profit from a few more explanations. In the first paragraph, introducing matrix decomposition might be inclusive, i.e., explaining that the product of factor matrices reconstruct the original matrix and why this is a non-trivial problem. In the third paragraph, it remains to be seen why there is a demand for tensor decomposition. The Statement of Need justifies the need through the non-existence of algorithm implementations. However, this justification needs more explanation for which problems to solve and for which target community these implementations are needed. Especially it would be relevant to explain the need in applications for algorithms provided in the submitted package but not in related works. This also provides the opportunity to integrate the very short Related Work section into the Statement of Need. While I appreciate the provided code example in the manuscript, it requires further explanations and a more coherent integration in the other sections. The plots should use identical colors and frequency axis to compare original and reconstructed data visually. Many citations and references do not follow the standards, are duplicates ("Zhang, Z. et al. in 2007 (Z. et al. Zhang, 2007)"), are missing Co-authors ("CICHOCK, 2009" should be "Cichock et al., 2009"), or are permuted ("Z. et al. Zhang, 2007"); most of those could be resolved by adding the full list of authors to the Bib file. DOIs should be added to the references, as suggested by the @editorialbot above. Overall, the language in the manuscript should be revised with a focus on rephrasing nested sentences and increasing coherence.

CeciliaCoelho commented 11 months ago

TL;DR

I recommend major revision of the paper and documentation available at the repository.

Overall review

There is evidence of the effort put in the package development however the documentation of the repository is a big downside due to being very small and poor (readme) or scattered in multiple files (example the contribution instructions). Not having instructions of how to use it or information on the examples included in the package in the readme can make users reluctant in trying this package due to the extra time it takes to search for all information they need to use it. This may sound harsh but I think such a nice package should have an equally nice and friendly readme. This will attract more users. Also, the paper is also lacking information and the summary information does not belong to the summary but rather to the statement of need. I advise the authors to check accepted papers and their repositories for a guideline.

Major comments

1 - The summary is too big in comparison to the rest of the documentation. The summary should describe concisely the package that is going to be presented stating what functions are implemented, some key features it contains and the target programming language. Right now the summary presented is more appropriate for the statement of need since it gives a background explanation of the implemented algorithms. The summary should be one paragraph. If the authors need some guidelines to fix the summary they should check accepted JOSS papers. 2 - The statement of need is very incomplete. It is missing a background explanation on the algorithms, what they are for and their applications. Having only a list of names with some references is very limited and at least a paragraph explaining each item should be included. 3 - The repository readme is very poor. It should have a brief explanation at the top stating what the repository has. It can be the summary used in the paper after fixing according to 2. It should clearly state how to use the functions provided and how to run the example code. The readme should also include the contributing.md. All information should be readily available to the users. Again I suggest the authors to check readme files of accepted papers if they need a guideline. 4 - The references need to be fully redone. The names of all the authors need to be written. Only when used in the text "et al." is used. It appears CICHOCK should be Cichocki. 5 - The Example section in the paper should be explained with more detail. Like what is the goal, the description of the problem 6 - The plots in Figure 1 are not consistent and cannot be used for comparison between them since they show different scales

Minor comments

7 - There are 2 license files. Please remove the extra one 8 - In the paper the authors use "I" and "We". Just one should be used in all paper

diehlpk commented 11 months ago

@kokitsuyuzaki please have a look at the comments above.

kokitsuyuzaki commented 11 months ago

Thank you for the review.

@kokitsuyuzaki please have a look at the comments above.

Sorry, I was on a long vacation and will check the review comments from now.

diehlpk commented 11 months ago

@kokitsuyuzaki Can you please let us know if you worked on the comments?

kokitsuyuzaki commented 11 months ago

Yes, I'm working on the comments.

This has been a difficult process due to many comments. Since many of the comments from two reviewers are duplicated, I have combined them as Issues. e.g., https://github.com/rikenbit/dcTensor/issues/8

I will reply to all of them in the next few days.

diehlpk commented 11 months ago

@kokitsuyuzaki just ping me and the reviewers here once you are done.

kokitsuyuzaki commented 11 months ago

I will contact you when all issues are addressed.

kokitsuyuzaki commented 10 months ago

@dekuenstle @CeciliaCoelho

I'm sorry for taking time so long. Now I have addressed all the issues, so please comment them. https://github.com/rikenbit/dcTensor/issues

kokitsuyuzaki commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

CeciliaCoelho commented 10 months ago

@editorialbot commands

editorialbot commented 10 months ago

Hello @CeciliaCoelho, here are the things you can ask me to do:


# List all available commands
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@editorialbot list editors

# Check the references of the paper for missing DOIs
@editorialbot check references

# Perform checks on the repository
@editorialbot check repository

# Adds a checklist for the reviewer using this command
@editorialbot generate my checklist

# Set a value for branch
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CeciliaCoelho commented 10 months ago

@kokitsuyuzaki thank you for addressing my comments. I now recommend acceptance.

dekuenstle commented 10 months ago

@kokitsuyuzaki thank you for the responses and changes. @diehlpk I recommend acceptance, too.

diehlpk commented 10 months ago

@kokitsuyuzaki I am traveling and will take care of the paper next week.

diehlpk commented 10 months ago

@editorialbot check references

editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/icdm.2007.99 is OK
- 10.3390/math9111189 is OK
- 10.1109/icassp.2007.367106 is OK
- 10.1109/cvpr.2007.383405 is OK
- 10.1038/44565 is OK
- 10.1186/s13059-019-1900-3 is OK
- 10.1142/9789812776136_0027 is OK
- 10.1093/nar/gks725 is OK
- 10.1007/978-3-642-15995-4_43 is OK
- 10.1093/bioinformatics/btv544 is OK

MISSING DOIs

- None

INVALID DOIs

- None
diehlpk commented 10 months ago

@editorialbot generate pdf

editorialbot commented 10 months ago

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

diehlpk commented 10 months ago

@kokitsuyuzaki

kokitsuyuzaki commented 10 months ago

Thanks, @diehlpk

I tagged the latest version as v1.2.3 and archieved by Zenodo.

The DOI is 10.5281/zenodo.8275544

Please also check these pages. https://github.com/rikenbit/dcTensor/releases/tag/v1.2.3 https://zenodo.org/record/8275544

diehlpk commented 10 months ago

@editorialbot set v1.2.3 as version

editorialbot commented 10 months ago

Done! version is now v1.2.3

diehlpk commented 10 months ago

@editorialbot generate pdf

diehlpk commented 10 months ago

@kokitsuyuzaki it seems the Zenodo entry does not match with the paper.

dcTensor: An R package for discrete matrix/tensor decomposition

kokitsuyuzaki

Yous should use your name and not your GitHub handle.

Can you please fix that?

Note there is no need to generate a new DOI.

editorialbot commented 10 months ago

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

diehlpk commented 10 months ago

@editorialbot set 10.5281/zenodo.8275544 as archive

editorialbot commented 10 months ago

Done! archive is now 10.5281/zenodo.8275544

kokitsuyuzaki commented 10 months ago

@diehlpk Sorry, I was having trouble mapping GitHub Release and Zenodo and couldn't come up with a solution other than to upgrade to a new version. I modified the author name. https://zenodo.org/record/8275544

diehlpk commented 10 months ago

@kokitsuyuzaki it looks good now.

diehlpk commented 10 months ago

@editorialbot recommend-accept

editorialbot commented 10 months ago 
Attempting dry run of processing paper acceptance...
editorialbot commented 10 months ago 
Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1109/icdm.2007.99 is OK
- 10.3390/math9111189 is OK
- 10.1109/icassp.2007.367106 is OK
- 10.1109/cvpr.2007.383405 is OK
- 10.1038/44565 is OK
- 10.1186/s13059-019-1900-3 is OK
- 10.1142/9789812776136_0027 is OK
- 10.1093/nar/gks725 is OK
- 10.1007/978-3-642-15995-4_43 is OK
- 10.1093/bioinformatics/btv544 is OK

MISSING DOIs

- None

INVALID DOIs

- None
editorialbot commented 10 months ago

:wave: @openjournals/dsais-eics, this paper is ready to be accepted and published.

Check final proof :point_right::page_facing_up: Download article

If the paper PDF and the deposit XML files look good in https://github.com/openjournals/joss-papers/pull/4501, then you can now move forward with accepting the submission by compiling again with the command @editorialbot accept

gkthiruvathukal commented 10 months ago

@editorialbot accept

editorialbot commented 10 months ago 
Doing it live! Attempting automated processing of paper acceptance...
editorialbot commented 10 months ago

Ensure proper citation by uploading a plain text CITATION.cff file to the default branch of your repository.

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``` cff-version: "1.2.0" authors: - family-names: Tsuyuzaki given-names: Koki orcid: "https://orcid.org/0000-0003-3797-2148" doi: 10.5281/zenodo.8275544 message: If you use this software, please cite our article in the Journal of Open Source Software. preferred-citation: authors: - family-names: Tsuyuzaki given-names: Koki orcid: "https://orcid.org/0000-0003-3797-2148" date-published: 2023-08-25 doi: 10.21105/joss.05664 issn: 2475-9066 issue: 88 journal: Journal of Open Source Software publisher: name: Open Journals start: 5664 title: "dcTensor: An R package for discrete matrix/tensor decomposition" type: article url: "https://joss.theoj.org/papers/10.21105/joss.05664" volume: 8 title: "dcTensor: An R package for discrete matrix/tensor decomposition" ```

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editorialbot commented 10 months ago

🐘🐘🐘 👉 Toot for this paper 👈 🐘🐘🐘

editorialbot commented 10 months ago

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editorialbot commented 10 months ago

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