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[REVIEW]: compareMCMCs: An R package for studying MCMC efficiency #3844

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whedon opened this issue Oct 22, 2021 · 54 comments
Closed
40 tasks done

[REVIEW]: compareMCMCs: An R package for studying MCMC efficiency #3844

whedon opened this issue Oct 22, 2021 · 54 comments
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accepted HTML published Papers published in JOSS R recommend-accept Papers recommended for acceptance in JOSS. review Stan

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@whedon
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whedon commented Oct 22, 2021

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

⚠️ JOSS reduced service mode ⚠️

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.

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/c9a34820bb5ccb0abb1a121312bf6272"><img src="https://joss.theoj.org/papers/c9a34820bb5ccb0abb1a121312bf6272/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/c9a34820bb5ccb0abb1a121312bf6272/status.svg)](https://joss.theoj.org/papers/c9a34820bb5ccb0abb1a121312bf6272)

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:

  1. Make sure you're logged in to your GitHub account
  2. Be sure to accept the invite at this URL: https://github.com/openjournals/joss-reviews/invitations

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

  • 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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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

  • 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.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • 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 and who the target audience is?
  • 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?

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

  • 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

General checks

  • Repository: Is the source code for this software available at the repository url?
  • License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
  • 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?
  • Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

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

  • 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.
  • Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
  • Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
  • Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
  • 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 and who the target audience is?
  • 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?
@whedon
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whedon commented Oct 22, 2021

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

  1. Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

watching

  1. You may also like to change your default settings for this watching repositories in your GitHub profile here: https://github.com/settings/notifications

notifications

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
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whedon commented Oct 22, 2021

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
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whedon commented Oct 22, 2021

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

 Can't find any papers to compile :-(

@fabian-s
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👋🏼 @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
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@whedon generate pdf from branch joss

@whedon
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whedon commented Oct 22, 2021

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

@whedon
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whedon commented Oct 22, 2021

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

@rowlandseymour
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rowlandseymour commented Oct 28, 2021

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
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whedon commented Nov 5, 2021

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

@whedon
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whedon commented Nov 5, 2021

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

@fabian-s
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fabian-s commented Nov 5, 2021

(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.

@perrydv
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perrydv commented Jan 12, 2022

@whedon check references

@whedon
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whedon commented Jan 12, 2022

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
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perrydv commented Jan 12, 2022

@whedon check references

@whedon
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whedon commented Jan 12, 2022

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
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perrydv commented Jan 13, 2022

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
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Thanks -- I see:
image

-- 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
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@whedon set 10.5281/zenodo.5842623 as archive

@whedon
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whedon commented Jan 13, 2022

OK. 10.5281/zenodo.5842623 is the archive.

@fabian-s
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@whedon set v1.0.0 as version

@whedon
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whedon commented Jan 13, 2022

OK. v1.0.0 is the version.

@perrydv
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perrydv commented Jan 13, 2022

@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
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@perrydv thanks, this works!

@fabian-s
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@whedon recommend-accept

@whedon whedon added the recommend-accept Papers recommended for acceptance in JOSS. label Jan 14, 2022
@whedon
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whedon commented Jan 14, 2022

Attempting dry run of processing paper acceptance...

@whedon
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whedon commented Jan 14, 2022

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
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whedon commented Jan 14, 2022

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

Check final proof 👉 openjournals/joss-papers#2886

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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
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@whedon accept deposit=true

@whedon whedon added accepted published Papers published in JOSS labels Jan 14, 2022
@whedon
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whedon commented Jan 14, 2022

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

@whedon
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whedon commented Jan 14, 2022

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

@whedon
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whedon commented Jan 14, 2022

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

  1. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.03844 joss-papers#2889
  2. Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03844
  3. If everything looks good, then close this review issue.
  4. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

@danielskatz
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Congratulations to @perrydv (Perry de Valpine) and co-authors!!

And thanks to @rowlandseymour @tbrown122387 for reviewing, and to @fabian-s for editing!
We couldn't do this without your efforts!

(and thanks specifically to @perrydv and @fabian-s - it's a pleasure for me as AEiC to get a paper that's completely ready for publishing, with no additional editing needed)

@whedon
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whedon commented Jan 14, 2022

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03844/status.svg)](https://doi.org/10.21105/joss.03844)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03844">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03844/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03844/status.svg
   :target: https://doi.org/10.21105/joss.03844

This is how it will look in your documentation:

DOI

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