editorialbot commented 9 months ago

Submitting author: !--author-handle-->@lrnv@osorensen<!--end-editor-- Reviewers: @lucaferranti, @AnderGray Archive: 10.5281/zenodo.6652672

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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

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✨ 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 @lucaferranti

📝 Checklist for @AnderGray

editorialbot commented 9 months ago

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editorialbot commented 9 months ago

Software report:

github.com/AlDanial/cloc v 1.88  T=0.06 s (1276.2 files/s, 94660.5 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Julia                           46            410            194           2448
TeX                              3             19              2            890
Markdown                        21            350              0            806
TOML                             3            136              1            593
YAML                             7              1              7            134
CSS                              1              0              0             17
-------------------------------------------------------------------------------
SUM:                            81            916            204           4888
-------------------------------------------------------------------------------

gitinspector failed to run statistical information for the repository

editorialbot commented 9 months ago

Wordcount for paper.md is 915

editorialbot commented 9 months ago

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

OK DOIs

- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.1201/9780367803896 is OK
- 10.1201/b18674 is OK
- 10.1214/07-AOS556 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 9 months ago

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

lucaferranti commented 9 months ago

Review checklist for @lucaferranti

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/lrnv/Copulas.jl?
[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 (@lrnv) 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 8 months ago

👋 @AnderGray, could you please update us on how it's going with your review?

lucaferranti commented 8 months ago

Hi @osorensen and @lrnv :wave: , overall very nice work and I definitely recommend acceptance, here are some comments.

Paper

Overall the paper is clear and gives a good motivation to the package.

It would be good to add a reference for DataGenCopulaBased.jl and BivariateCopulas.jl, especially since both are registered in zenodo.
At line 40 a pretty strong statement is made

Copulas.jl is clearly the must fully featured, and brings, as a key feature, the complience with the broader ecosystem.

it is not clear to me from tha paper alone that Copulas.jl is the most feature complete of the three and would be good to give some more arguments in the paper. Ideally, a table comparing features of the three would be nice to have.

Documentation

Overall the API is well documented and gives a lot of background knowledge. A few improvement suggestions

Currently the documentation feels to have more theory than code, it would be nice to expand the Examples section with a few more examples of how to use the code, ideally within some applications of how to solve some "real-world" problems. E.g. applying Copulas.jl to some popular datasets and concrete example problems.
In the turing integration example, the code ends with a plot, would be good to include the resulting image in the documentation. If possible, some visual representation would also be nice to have for the example of the README
The contribution guidelines section is very short, but I think this is enough. Since you have the colprac badge, you could add a sentence there saying that more info can be found in the ColPrac guide.

Typos

I spotted a few typos, you may consider using a tool like typos-cli to check more systematically. This could also be setup on CI (actually the julia repo does it) but it might be an overkill.

line 40 of the paper must -> most
line 41 of the paper complience -> compliance
line 46 of the paper specify -> specifies
line 55 folloiwng -> following (I also think consists of is the grammatically correct form, instead of is consisting of but I am not native)
line 63 exploit -> exploits
Documentation navbar Exemples -> Examples
here in the "Unfinished work" box, wtill -> still

Unicode

The paper has some issues rendering some unicode characters

lrnv commented 8 months ago

@lucaferranti Thanks a lot for your time and your review. I definitely agree with all the points you mentioned, 100%.

I will split your review into issues on Copulas.jl to be able to start working on each of them with my co-author @Santymax98. @osorensen it might take a while, but I think it is definitely worth it.

lucaferranti commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

lrnv commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

AnderGray commented 8 months ago

@osorensen @lrnv Hi 👋 you can expect my review this week. Overall, looks good

AnderGray commented 8 months ago

Review checklist for @AnderGray

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/lrnv/Copulas.jl?
[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 (@lrnv) 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

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] 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?
[x] 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

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] 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?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] 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?

osorensen commented 8 months ago

Thanks a lot for your reviews @lucaferranti and @AnderGray!

lrnv commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

lrnv commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

lrnv commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

lrnv commented 8 months ago

@editorialbot generate pdf

editorialbot commented 8 months ago

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

lrnv commented 8 months ago

There we are; @lucaferranti we are almost done with your review, you can check out the list of tickets we have here : https://github.com/lrnv/Copulas.jl/issues/114 There are only two big tickets remaining, expected time one to two weeks. @osorensen is that acceptable timing ?

lucaferranti commented 8 months ago

@lrnv looks very good! I think it's approaching convergence and looking forward to see teh final result after the fixes. I left an issue https://github.com/lrnv/Copulas.jl/issues/135 with a few minor improvement suggestions for the benchmarking table

lucaferranti commented 8 months ago

oh in the comparison table of libraries there's a small typographic issue

but I am not sure if that can be fixed in any way in plain markdown, might have we just have to cope with it :/

lrnv commented 8 months ago

@editorialbot generate pdf

lrnv commented 8 months ago

@lucaferranti thanks, done. Markdown tables are indeed an obscure thing...

editorialbot commented 8 months ago

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

osorensen commented 8 months ago

There we are; @lucaferranti we are almost done with your review, you can check out the list of tickets we have here : lrnv/Copulas.jl#114 There are only two big tickets remaining, expected time one to two weeks. @osorensen is that acceptable timing ?

Absolutely! It's also fine if it takes longer time, but in that case it would be great if you kept us updated on the progress.

AnderGray commented 8 months ago

Hi @lrnv and @osorensen! A very useful (and needed) tool in Julia. The documentation is also quite comprehensive and well written, and will serve as a good resource for those reading up or learning about copulas. Acceptance is certainly recommended.

Paper

This sentence could be confusing Copulas being fundamentally distributions of random vectors. Maybe rephrase to something like: Since copulas can combine arbitrary distributions to form correlated random vectors …
Line 33 our code expressiveness and tidiness -> our code’s …
Line 44 we did not consider … -> we have not considered …
In the example 1., there is a bug. I think you want either x = rand(X,1000) or D = SklarDist(C,(X1,X2,X3))

With the above fix, I still get an error, related to fitting the binomial distribution

ERROR: suffstats is not implemented for (Binomial, Vector{Float64}).
Stacktrace:
[1] error(s::String)
@ Base ./error.jl:35
[2] suffstats(dt::Type{Binomial}, xs::Vector{Float64})
@ Distributions ~/.julia/packages/Distributions/UaWBm/src/genericfit.jl:5
[3] fit_mle(dt::Type{Binomial}, x::Vector{Float64})
@ Distributions ~/.julia/packages/Distributions/UaWBm/src/genericfit.jl:27
[4] fit(dt::Type{Binomial}, x::Vector{Float64})
@ Distributions ~/.julia/packages/Distributions/UaWBm/src/genericfit.jl:33
[5] (::Copulas.var"#12#13"{Tuple{Gamma, Normal, Binomial}, Matrix{Float64}})(i::Int64)
@ Copulas ./cartesian.jl:0
[6] iterate
@ ./generator.jl:47 [inlined]
[7] collect_to!(dest::Vector{Distribution{Univariate, Continuous}}, itr::Base.Generator{UnitRange{Int64}, Copulas.var"#12#13"{Tuple{Gamma, Normal, Binomial}, Matrix{Float64}}}, offs::Int64, st::Int64)
@ Base ./array.jl:840
[8] collect_to!(dest::Vector{Gamma{Float64}}, itr::Base.Generator{UnitRange{Int64}, Copulas.var"#12#13"{Tuple{Gamma, Normal, Binomial}, Matrix{Float64}}}, offs::Int64, st::Int64)
@ Base ./array.jl:848
[9] collect_to_with_first!(dest::Vector{Gamma{Float64}}, v1::Gamma{Float64}, itr::Base.Generator{UnitRange{Int64}, Copulas.var"#12#13"{Tuple{Gamma, Normal, Binomial}, Matrix{Float64}}}, st::Int64)
@ Base ./array.jl:818
[10] collect(itr::Base.Generator{UnitRange{Int64}, Copulas.var"#12#13"{Tuple{Gamma, Normal, Binomial}, Matrix{Float64}}})
@ Base ./array.jl:792
[11] _totuple
@ ./tuple.jl:401 [inlined]
[12] Tuple
@ ./tuple.jl:369 [inlined]
[13] fit(#unused#::Type{SklarDist{FrankCopula, Tuple{Gamma, Normal, Binomial}}}, x::Matrix{Float64})
@ Copulas ~/Documents/julia/Copulas_review/Copulas.jl/src/SklarDist.jl:70
[14] top-level scope
@ REPL[10]:1

# Although you'll probbaly get a bad fit ! -> typo in probably
line 60 has seen -> have seen
“# Add the loglikelyhood to the model -> typo in loglikelihood

The Generator example fails, perhaps you forgot to export?

ERROR: UndefVarError: `Generator` not defined
Stacktrace:
[1] top-level scope
@ REPL[5]:1

Docs

I agree with Luca that the docs could benefit from more code examples. Additionally, here’s a couple of typos I’ve found when reading through the docs:

There is a typo in the folder name: exemples -> examples
for random ve tors and random variables -> vectors in https://github.com/lrnv/Copulas.jl/blob/6d5f5c5f3ca9724a2feba33612e404a0b0388a7e/docs/src/getting_started.md?plain=1#L102
In the first example, you say: Increase the number of observations to get a beter fit (or not?). Are you getting a bad fit because you've changed the distribution function Maybe it’s better to have a simpler example where you fit re-fit the Clayton? Also beter -> better
“SUite” -> “Suite”
Anticonomotony -> anticomonotony in https://github.com/lrnv/Copulas.jl/blob/6d5f5c5f3ca9724a2feba33612e404a0b0388a7e/docs/src/dependence_measures.md?plain=1#L36
The transformation, wich is called the inverse williamson transformation -> which and Williamson in https://github.com/lrnv/Copulas.jl/blob/6d5f5c5f3ca9724a2feba33612e404a0b0388a7e/src/Generator/WilliamsonGenerator.jl#L14
Missing a close bracket in equation for InvGaussianGenerator in https://github.com/lrnv/Copulas.jl/blob/32d1ac56383f9da386f05d3992c6fe518e447125/src/Generator/UnivariateGenerator/InvGaussianGenerator.jl#L15

Features

Copulas.jl is very feature complete, including many different types of copulas (elliptical, empirical, Archimedean), and also allows you to create your own copulas using generators. The Williamson transformation is also a very nice idea! Although not required for acceptance of this paper/package, there's a couple suggested "good to have" features

Conditioning: in BivariateCopulas.jl we perform conditioning of copulas and joint distributions using numerical finite differencing. Not sure if there's a better way to do it, but it allows you to sample from arbitrary (without a family) copulas and distributions. I think this is needed if you want to do implement vines
Rossenblat (and inverse) transformation is often used in uncertainty analysis (particularly reliability analysis) to transform random variables into independent standard normal variables.
Plotting / Visualisation

lrnv commented 8 months ago

Thanks @AnderGray for your time, your review, and your ideas. I definitely agree with all of your comments and suggestions for Copulas.jl. Let met first take a moment to move all your comments into separated issues on the repo, after what you will be able to track progress at this particular link.

osorensen commented 8 months ago

@lucaferranti I notice that there is one unchecked item in your review checklist, related to example usage. Has this been addressed by @lrnv by now, or is there something more than should be done?

lrnv commented 7 months ago

@osorensen this is still on my checklist but we are working on it. @lucaferranti I think this relates to https://github.com/lrnv/Copulas.jl/issues/117 ?

@AnderGray By the way, we are thinking with my coauthor that the feature requests you made in your review will take a long time to solve. They are clearly relevant and important, and we will keep them as issues to be solved in the future, but maybe they should not be blocking for the publication of the paper. What do you three @AnderGray @lucaferranti and @osorensen think about that ? I am talking specifically of issues https://github.com/lrnv/Copulas.jl/issues/150 https://github.com/lrnv/Copulas.jl/issues/151 and https://github.com/lrnv/Copulas.jl/issues/152

AnderGray commented 7 months ago

@lrnv Correct, those suggestions are not required for publication

lucaferranti commented 7 months ago

@osorensen this is still on my checklist but we are working on it. @lucaferranti I think this relates to lrnv/Copulas.jl#117 ?

Correct the box I havent ticked yet is waiting for that issue.

osorensen commented 7 months ago

Thanks to both of you for the quick response!

lucaferranti commented 7 months ago

@osorensen all my comments have been addressed and the paper is ready from my side

osorensen commented 7 months ago

Thanks @lucaferranti!

osorensen commented 7 months ago

@editorialbot check references

osorensen commented 7 months ago

@editorialbot generate pdf

editorialbot commented 7 months ago

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

OK DOIs

- 10.18637/jss.v021.i04 is OK
- 10.18637/jss.v034.i09 is OK
- 10.18637/jss.v039.i09 is OK
- 10.1201/9780367803896 is OK
- 10.1201/b18674 is OK
- 10.1214/07-AOS556 is OK
- 10.18637/jss.v098.i16 is OK
- 10.5281/zenodo.2647458 is OK
- 10.5281/zenodo.7944064 is OK
- 10.5281/zenodo.10412898 is OK

MISSING DOIs

- None

INVALID DOIs

- None

editorialbot commented 7 months ago

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

osorensen commented 7 months ago

@lrnv, as you note I have made a number of small issues and PRs which need to be fixed before we can move on with accepting the paper.

Anyway, congratulations with what seems to be an excellent package and a well-written paper.

lrnv commented 7 months ago

@AnderGray Maybe you could help with lrnv/Copulas.jl#176 ?

lrnv commented 7 months ago

@editorialbot set v0.1.21 as version

editorialbot commented 7 months ago

Done! version is now v0.1.21

osorensen commented 7 months ago

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Double check authors and affiliations (including ORCIDs)
Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
Archive the release on Zenodo/figshare/etc and post the DOI here.
Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
Make sure that the license listed for the archive is the same as the software license.

Editor Tasks Prior to Acceptance

[x] Read the text of the paper and offer comments/corrections (as either a list or a pull request)
[ ] Check that the archive title, author list, version tag, and the license are correct
[ ] Set archive DOI with @editorialbot set <DOI here> as archive
[ ] Set version with @editorialbot set <version here> as version
[ ] Double check rendering of paper with @editorialbot generate pdf
[ ] Specifically check the references with @editorialbot check references and ask author(s) to update as needed
[ ] Recommend acceptance with @editorialbot recommend-accept

osorensen commented 7 months ago

@lrnv, can you now please complete these tasks?

[x] Double check authors and affiliations (including ORCIDs)
[x] Make a release of the software with the latest changes from the review and post the version number here. This is the version that will be used in the JOSS paper.
[x] Archive the release on Zenodo/figshare/etc and post the DOI here.
[x] Make sure that the title and author list (including ORCIDs) in the archive match those in the JOSS paper.
[x] Make sure that the license listed for the archive is the same as the software license.

openjournals / joss-reviews

[REVIEW]: Copulas.jl: A fully Distributions.jl-compliant copula package #6189

Status

Reviewer instructions & questions

Checklists

Review checklist for @lucaferranti

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Paper

Documentation

Typos

Unicode

Review checklist for @AnderGray

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Paper

Docs

Features

Post-Review Checklist for Editor and Authors

Additional Author Tasks After Review is Complete

Editor Tasks Prior to Acceptance