[REVIEW]: BGGM: Bayesian Gaussian Graphical Models in R

whedon commented 4 years ago

Submitting author: @donaldRwilliams (Donald Williams ) Repository: https://github.com/donaldRwilliams/BGGM Version: 1.0.0 Editor: @akeshavan Reviewer: @jayrobwilliams, @paulgovan Archive: 10.5281/zenodo.3954503

Status

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Markdown: [![status](https://joss.theoj.org/papers/4ecb84c5b3b2a2b5da46be4e0700502f/status.svg)](https://joss.theoj.org/papers/4ecb84c5b3b2a2b5da46be4e0700502f)

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

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

Make sure you're logged in to your GitHub account
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 @akeshavan know.

✨ Please try and complete your review in the next two weeks ✨

Review checklist for @jayrobwilliams

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 (@donaldRwilliams) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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 @paulgovan

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 (@donaldRwilliams) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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: Do the authors clearly state 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?

arfon commented 4 years ago

@whedon accept

whedon commented 4 years ago

Attempting dry run of processing paper acceptance...

whedon commented 4 years ago

Reference check summary:

OK DOIs

- 10.3758/s13423-016-1221-4 is OK
- 10.1177/0013164416669201 is OK
- 10.31234/OSF.IO/X8DPR is OK
- 10.31234/osf.io/ypxd8 is OK
- 10.1080/00031305.2018.1549100 is OK
- 10.1016/j.csda.2007.09.008 is OK
- 10.1037/abn0000446 is OK
- 10.1080/00273171.2019.1640103 is OK
- 10.1214/009053606000000821 is OK
- 10.1037/met0000254 is OK
- 10.1214/17-BA1092 is OK
- 10.1214/07-AOAS107 is OK
- 10.3758/s13423-016-1221-4 is OK
- 10.1037/met0000201 is OK
- 10.1080/10618600.2012.679239 is OK
- 10.1080/01621459.1993.10476321 is OK
- 10.1007/bf00162520 is OK
- 10.1191/1471082x04st063oa is OK
- 10.1080/01621459.1988.10478640 is OK
- 10.21236/ada241408 is OK
- 10.1198/004017008000000064 is OK
- 10.21105/joss.00026 is OK
- 10.31234/osf.io/p69m7 is OK
- 10.1214/aos/1176346785 is OK
- 10.31234/osf.io/zw7pf is OK
- 10.3758/s13428-017-0910-x is OK
- 10.1080/00273171.2019.1614898 is OK
- 10.1214/13-ejs854 is OK
- 10.1109/vetecs.2005.1543265 is OK
- 10.18637/jss.v048.i04 is OK
- 10.18637/jss.v089.i03 is OK
- fpsyg.2019.01050 is OK
- 10.1080/00273171.2020.1716673 is OK
- 10.31234/osf.io/4kfjp is OK
- 10.1063/1.4870402 is OK
- 10.1186/1752-0509-3-55 is OK
- 10.1007/s41109-020-0251-z is OK
- 10.1093/biostatistics/kxt005 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 4 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/1584

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1584, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 4 years ago

@whedon accept deposit=true

whedon commented 4 years ago

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

whedon commented 4 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 4 years ago

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

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1585
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02111
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 4 years ago

@jayrobwilliams, @paulgovan - many thank for your reviews here and to @akeshavan for editing this submission ✨

@donaldRwilliams - your paper is now accepted into JOSS :zap::rocket::boom:

whedon commented 4 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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.02111/status.svg)](https://doi.org/10.21105/joss.02111)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02111">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02111/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02111/status.svg
   :target: https://doi.org/10.21105/joss.02111

This is how it will look in your documentation:

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