[REVIEW]: compareMCMCs: An R package for studying MCMC efficiency

whedon commented 2 years ago

Submitting author: @perrydv (Perry de Valpine) Repository: https://github.com/nimble-dev/compareMCMCs/ Version: v1.0.0 Editor: @fabian-s Reviewer: @rowlandseymour, @tbrown122387 Archive: 10.5281/zenodo.5842623

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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

@rowlandseymour & @tbrown122387, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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The reviewer guidelines are available here: https://joss.readthedocs.io/en/latest/reviewer_guidelines.html. Any questions/concerns please let @fabian-s 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 ✨

Review checklist for @rowlandseymour

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@perrydv) 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

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 and who the target audience is?
[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?

Review checklist for @tbrown122387

✨ Important: Please do not use the Convert to issue functionality when working through this checklist, instead, please open any new issues associated with your review in the software repository associated with the submission. ✨

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 repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@perrydv) 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

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 and who the target audience is?
[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?

whedon commented 2 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @rowlandseymour, @tbrown122387 it looks like you're currently assigned to review this paper :tada:.

: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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whedon commented 2 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.04 s (692.1 files/s, 98679.8 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
R                               20            172            590           1554
HTML                             3             37              6            668
Rmd                              2            174            301            170
Markdown                         1             11              0             24
-------------------------------------------------------------------------------
SUM:                            26            394            897           2416
-------------------------------------------------------------------------------

Statistical information for the repository 'c6c82175077fe5017f26a53e' was
gathered on 2021/10/22.
No commited files with the specified extensions were found.

whedon commented 2 years ago

PDF failed to compile for issue #3844 with the following error:

 Can't find any papers to compile :-(

fabian-s commented 2 years ago

👋🏼 @tbrown122387 @perrydv @rowlandseymour this is the review thread for the paper. All of our communications will happen here from now on.

Both reviewers have checklists at the top of this thread 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 openjournals/joss-reviews#3844 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 reviews to be completed within about 2-4 weeks. Please let me know if any of you require some more time. We can also use Whedon (our bot) to set automatic reminders if you know you'll be away for a known period of time.

Please feel free to ping me (@fabian-s) if you have any questions/concerns.

fabian-s commented 2 years ago

@whedon generate pdf from branch joss

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon commented 2 years ago

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

rowlandseymour commented 2 years ago

I spent yesterday afternoon playing around with the compareMCMCs package and it's really nice. The functionality is good, and I found the vignette very helpful in describing how everything works. The actual R code itself is also well documented and the whole package seems stable.

I've raised a few issues which I'd say are minor issues. The one improvement I'd really like to see is an example of Stan code in the vignette. Once these issues are all resolved I'm happy for the paper to be accepted. Fantastic work!

whedon commented 2 years ago

:wave: @rowlandseymour, please update us on how your review is going (this is an automated reminder).

whedon commented 2 years ago

:wave: @tbrown122387, please update us on how your review is going (this is an automated reminder).

fabian-s commented 2 years ago

(sorry about those automatic reminders...)

@perrydv both reviewers have gone through their checklists and defined some issues in your repo.

I would consider

nimble-dev/compareMCMCs#16 nimble-dev/compareMCMCs#17 nimble-dev/compareMCMCs#18

to be issues currently blocking acceptance as they are directly relevant for points on the JOSS criteria checklist. Your package currently also violates many community standards for best practice R packages, see nimble-dev/compareMCMCs#26.

Please adress/discuss the issues opened by the reviewers and me in the respective issue threads.

fabian-s commented 2 years ago

@perrydv please update us on your progress adressing these issues.

perrydv commented 2 years ago

@fabian-s Apologies for the delay and I am working on it now.

fabian-s commented 2 years ago

@perrydv please let us know what your timeline for adressing the remaining issues is

perrydv commented 2 years ago

@fabian-s Thanks for pinging me on this. I think all issues are now handled with corresponding replies on the github issues threads.

tbrown122387 commented 2 years ago

All my checklist boxes are checked @fabian-s so we're good to go on my end

rowlandseymour commented 2 years ago

All my checklists boxes are now checked too @fabian-s, all my comments have been resolved.

fabian-s commented 2 years ago

@tbrown122387 @rowlandseymour thank you both for your reviews and your quick reaction!

fabian-s commented 2 years ago

@whedon generate pdf from branch joss

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

fabian-s commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

whedon commented 2 years ago

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

OK DOIs

- 10.21105/joss.01722 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.5281/zenodo.1211190 is OK
- 10.18637/jss.v095.i07 is OK
- 10.21105/joss.00640 is OK
- 10.7717/peerj-cs.55 is OK

MISSING DOIs

- 10.1002/sim.3680 may be a valid DOI for title: The BUGS project: Evolution, critique and future directions
- 10.18637/jss.v042.i09 may be a valid DOI for title: MCMCpack: Markov Chain Monte Carlo in R

INVALID DOIs

- None

fabian-s commented 2 years ago

@perrydv

Almost done :partying_face: -- at this point could you please:

[x] Add the missing DOIs for BUGS and MCMCpack to your references (see above)
[x] Make a tagged release of your software, and list the version tag of the archived version here.
[x] Archive the reviewed software in Zenodo or a similar service (e.g., figshare, an institutional repository)
[x] Check the archival deposit (e.g., in Zenodo) has the correct metadata. This includes the title (should match the paper title) and author list (make sure the list is correct and people who only made a small fix are not on it). You may also add the authors' ORCID.
[x] Please list the DOI of the archived version here.

I can then move forward with accepting the submission.

perrydv commented 2 years ago

Thanks @fabian-s. Can you help me understand what is the best step in the process to put our package on CRAN? After all of the above steps, so that we can then list the resulting JOSS publication as the CITATION request for the package?

fabian-s commented 2 years ago

For that [EDIT: the CITATION] you'll need the DOI of the JOSS paper, which is already given on your draft? Not sure I really understand the question, sorry -- having a JOSS publication and getting on CRAN seem to be unrelated to me.

tbrown122387 commented 2 years ago

@perrydv once were all finished with the Review stuff, it spits out something like this almost immediately https://joss.theoj.org/papers/10.21105/joss.02599 and you just throw the bibtex data into CITATION

perrydv commented 2 years ago

@whedon generate pdf from branch joss

whedon commented 2 years ago

Attempting PDF compilation from custom branch joss. Reticulating splines etc...

whedon commented 2 years ago

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

perrydv commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.21105/joss.01722 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.5281/zenodo.1211190 is OK
- 10.18637/jss.v095.i07 is OK
- 10.21105/joss.00640 is OK
- 10.7717/peerj-cs.55 is OK

MISSING DOIs

- 10.1002/sim.3680 may be a valid DOI for title: The BUGS project: Evolution, critique and future directions
- 10.18637/jss.v042.i09 may be a valid DOI for title: MCMCpack: Markov Chain Monte Carlo in R

INVALID DOIs

- None

perrydv commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.21105/joss.01722 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.5281/zenodo.1211190 is OK
- 10.18637/jss.v095.i07 is OK
- 10.21105/joss.00640 is OK
- 10.1002/sim.3680 is OK
- 10.1023/A:1008929526011 is OK
- 10.7717/peerj-cs.55 is OK

MISSING DOIs

- 10.18637/jss.v042.i09 may be a valid DOI for title: MCMCpack: Markov Chain Monte Carlo in R

INVALID DOIs

- None

perrydv commented 2 years ago

@whedon check references

whedon commented 2 years ago

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

OK DOIs

- 10.21105/joss.01722 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.5281/zenodo.1211190 is OK
- 10.18637/jss.v095.i07 is OK
- 10.21105/joss.00640 is OK
- 10.1002/sim.3680 is OK
- 10.1023/A:1008929526011 is OK
- 10.7717/peerj-cs.55 is OK
- 10.18637/jss.v042.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

perrydv commented 2 years ago

Thanks @fabian-s. I've done the following:

Fixed a formatting detail in the vignette.
Added three DOIs to paper.bib and re-ran whedon to build the pdf and check the DOIs.
Tagged a release as v1.0.0 on GitHub.
Archived the release on Zenodo.
Found where to update author names in Zenodo metadata and title to match the paper title.
The DOI from Zenodo is: 10.5281/zenodo.5842623

The process is new to me and I was not sure whether to take the (permanent) step of hitting publish on Zenodo.

fabian-s commented 2 years ago

Thanks -- I see:

-- we prefer that the software author names match those on the JOSS paper. Is there a reason you didn't use your real name instead of perrydv?

fabian-s commented 2 years ago

@whedon set 10.5281/zenodo.5842623 as archive

whedon commented 2 years ago

OK. 10.5281/zenodo.5842623 is the archive.

fabian-s commented 2 years ago

@whedon set v1.0.0 as version

whedon commented 2 years ago

OK. v1.0.0 is the version.

perrydv commented 2 years ago

@fabian-s Zenodo did something where it automatically populated metadata and took my GitHub user name (perrydv) instead of my real name. I thought I fixed that when I updated the metadata. Also I thought I updated the title to match the paper title as requested. I went back into that and tried save and publish. Does this help: https://zenodo.org/record/5842623. Sorry I'm new to this and not sure I've done it right.

fabian-s commented 2 years ago

@perrydv thanks, this works!

fabian-s commented 2 years ago

@whedon recommend-accept

whedon commented 2 years ago

Attempting dry run of processing paper acceptance...

whedon commented 2 years ago

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

OK DOIs

- 10.21105/joss.01722 is OK
- 10.1080/10618600.2016.1172487 is OK
- 10.5281/zenodo.1211190 is OK
- 10.18637/jss.v095.i07 is OK
- 10.21105/joss.00640 is OK
- 10.1002/sim.3680 is OK
- 10.1023/A:1008929526011 is OK
- 10.7717/peerj-cs.55 is OK
- 10.18637/jss.v042.i09 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 2 years ago

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

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2886

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2886, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

danielskatz commented 2 years ago

@whedon accept deposit=true

whedon commented 2 years ago

Doing it live! Attempting automated processing of paper acceptance...

openjournals / joss-reviews