[REVIEW]: Additive Bayesian Networks

editorialbot commented 4 weeks ago

Submitting author: !--author-handle-->@matteodelucchi@crvernon<!--end-editor-- Reviewers: @dhvalden, @abhishektiwari Archive: Pending

Status

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Reviewers and authors:

Please avoid lengthy details of difficulties in the review thread. Instead, please create a new issue in the target repository and link to those issues (especially acceptance-blockers) by leaving comments in the review thread below. (For completists: if the target issue tracker is also on GitHub, linking the review thread in the issue or vice versa will create corresponding breadcrumb trails in the link target.)

Reviewer instructions & questions

@dhvalden & @abhishektiwari, your review will be checklist based. Each of you will have a separate checklist that you should update when carrying out your review. First of all you need to run this command in a separate comment to create the checklist:

@editorialbot generate my checklist

The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @crvernon know.

✨ Please start on your review when you are able, and be sure to complete your review in the next six weeks, at the very latest ✨

Checklists

📝 Checklist for @abhishektiwari

editorialbot commented 4 weeks ago

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editorialbot commented 4 weeks ago

Software report:

github.com/AlDanial/cloc v 1.90  T=0.12 s (1219.2 files/s, 358428.3 lines/s)
--------------------------------------------------------------------------------
Language                      files          blank        comment           code
--------------------------------------------------------------------------------
R                                56           2320           5291          11694
C                                20           2067           2941           7651
Bourne Shell                      2            322            374           2263
YAML                             12             91             74           1545
Markdown                          9            494              0           1368
TeX                               3            134              2           1303
C++                              12            204            358            667
SVG                               1             75              1            397
C/C++ Header                     20            146             34            306
Rmd                               8            237            628            147
m4                                1              3              0             18
JSON                              1              0              0             17
Bourne Again Shell                1              6              2             14
make                              1              5              3             13
--------------------------------------------------------------------------------
SUM:                            147           6104           9708          27403
--------------------------------------------------------------------------------

Commit count by author:

   143  Jonas I. Liechti
    89  Matteo Delucchi
    19  Jonas Liechti
     4  j-i-l
     3  reinhardfurrer
     2  matteodelucchi

editorialbot commented 4 weeks ago

Paper file info:

📄 Wordcount for paper.md is 1322

🔴 Failed to discover a Statement of need section in paper

editorialbot commented 4 weeks ago

License info:

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

editorialbot commented 4 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 4 weeks ago

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

OK DOIs

- 10.3389/fvets.2020.00073 is OK
- 10.1016/j.actatropica.2017.04.034 is OK
- 10.1186/s12917-019-1965-y is OK
- 10.1016/j.compbiomed.2022.105740 is OK
- 10.18637/jss.v105.i08 is OK
- 10.18637/jss.v047.i11 is OK
- 10.18637/jss.v008.i20 is OK
- 10.1093/bioinformatics/btw807 is OK
- 10.18637/jss.v046.i10 is OK
- 10.1007/s10614-020-10065-7 is OK
- 10.1016/j.ijar.2022.09.004 is OK
- 10.1007/s10462-022-10351-w is OK
- 10.18637/jss.v035.i03 is OK
- 10.18637/jss.v067.i01 is OK
- 10.18129/B9.bioc.graph is OK
- 10.18129/B9.bioc.Rgraphviz is OK
- 10.18637/jss.v103.i02 is OK

MISSING DOIs

- No DOI given, and none found for title: Information-Theoretic Scoring Rules to Learn Addit...
- No DOI given, and none found for title: R: A Language and Environment for Statistical Comp...
- No DOI given, and none found for title: rjags: Bayesian Graphical Models using MCMC
- No DOI given, and none found for title: Modern Applied Statistics with S
- No DOI given, and none found for title: doParallel: Foreach Parallel Adaptor for the ’para...
- No DOI given, and none found for title: foreach: Provides Foreach Looping Construct
- No DOI given, and none found for title: mclogit: Multinomial Logit Models, with or without...
- No DOI given, and none found for title: Rcpp: Seamless R and C++ Integration
- No DOI given, and none found for title: RcppArmadillo: ’Rcpp’ Integration for the ’Armadil...
- 10.1016/j.csda.2013.04.014 may be a valid DOI for title: Bayesian computing with INLA: New features.
- No DOI given, and none found for title: GNU Scientific Library Reference Manual (3rd Ed.)
- No DOI given, and none found for title: JAGS: A Program for Analysis of Bayesian Graphical...
- 10.32614/rj-2011-002 may be a valid DOI for title: testthat: Get Started with Testing

INVALID DOIs

- None

crvernon commented 4 weeks ago

👋 @matteodelucchi, @dhvalden, and @abhishektiwari - This is the review thread for the paper. All of our communications will happen here from now on.

Please read the "Reviewer instructions & questions" in the first comment above.

Both reviewers have checklists at the top of this thread (in that first comment) with the JOSS requirements. As you go over the submission, please check any items that you feel have been satisfied. There are also links to the JOSS reviewer guidelines.

The JOSS review is different from most other journals. Our goal is to work with the authors to help them meet our criteria instead of merely passing judgment on the submission. As such, the reviewers are encouraged to submit issues and pull requests on the software repository. When doing so, please mention https://github.com/openjournals/joss-reviews/issues/6822 so that a link is created to this thread (and I can keep an eye on what is happening). Please also feel free to comment and ask questions on this thread. In my experience, it is better to post comments/questions/suggestions as you come across them instead of waiting until you've reviewed the entire package.

We aim for the review process to be completed within about 4-6 weeks but please make a start well ahead of this as JOSS reviews are by their nature iterative and any early feedback you may be able to provide to the author will be very helpful in meeting this schedule.

abhishektiwari commented 4 weeks ago

Review checklist for @abhishektiwari

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

[x] I confirm that I read and will adhere to the JOSS code of conduct.

General checks

[x] Repository: Is the source code for this software available at the https://github.com/furrer-lab/abn?
[x] License: Does the repository contain a plain-text LICENSE or COPYING file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@matteodelucchi) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines
[x] Data sharing: If the paper contains original data, data are accessible to the reviewers. If the paper contains no original data, please check this item.
[x] Reproducibility: If the paper contains original results, results are entirely reproducible by reviewers. If the paper contains no original results, please check this item.
[x] Human and animal research: If the paper contains original data research on humans subjects or animals, does it comply with JOSS's human participants research policy and/or animal research policy? If the paper contains no such data, please check this item.

Functionality

[ ] Installation: Does installation proceed as outlined in the documentation?
[ ] Functionality: Have the functional claims of the software been confirmed?
[ ] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[ ] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[ ] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[ ] A statement of need: Does the paper have a section titled 'Statement of need' that clearly states what problems the software is designed to solve, who the target audience is, and its relation to other work?
[ ] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[ ] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[ ] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

abhishektiwari commented 2 weeks ago

@matteodelucchi I am unable to progress with review as installation instruction don't work as described. Please see this ticket

matteodelucchi commented 2 weeks ago

@matteodelucchi I am unable to progress with review as installation instruction don't work as described. Please see this ticket

Thanks for bringing this up, @abhishektiwari! I have addressed your concern in this pull request, which should clarify the installation instructions.

crvernon commented 1 day ago

👋 @matteodelucchi, @dhvalden, and @abhishektiwari - just checking in to see how things are going with this review. Could you each provide a short update response in this thread? Thanks!

openjournals / joss-reviews