[REVIEW]: latentcor: An R Package for estimating latent correlations from mixed data types

whedon commented 3 years ago

Submitting author: @muellsen (Christian Lorenz Müller) Repository: https://github.com/mingzehuang/latentcor Version: v1.1.0 Editor: @crvernon Reviewer: @corybrunson, @rmflight Archive: 10.5281/zenodo.5517823

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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

@corybrunson & @rmflight , 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 @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 ✨

Review checklist for @corybrunson

✨ 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 (@muellsen) 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 @rmflight

✨ 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 (@muellsen) 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?

mingzehuang commented 3 years ago

@crvernon Thank you very much! I've fixed the DOI. The author names and affiliations are correct:)

crvernon commented 3 years ago

@mingzehuang we are almost there! Next is just setting up the archive for your new release. Since there have not been any releases yet in your repo, here are a few pointers:

I find Zenodo easy to use to mint a DOI (permanent archive identifier) for each GitHub release. You will likely need to create a free Zenodo account and link your GitHub repository to it. Then once linked, you can conduct your release on GitHub and it will automatically trigger Zenodo to mint a DOI for you. If you want the DOI as a badge, you can add that as well. There are other options for creating a permanent archive resulting in a DOI for your code as well. Don't hesitate to reach out if you have questions.
We want to make sure the archival has the correct metadata that JOSS requires. This includes a title that matches the paper title and a correct author list.

So here is what we have left to do:

[x] Conduct a GitHub release of the current reviewed version of the software you now have on the master and 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) to ensure it has the correct metadata. This includes the title (should match the paper title) and author list. 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.

mingzehuang commented 3 years ago

@crvernon Thank you so much! I've tried to create it! Here is the DOI: 10.5281/zenodo.5517823 Let me know if there is anything need to be correct:)

muellsen commented 3 years ago

Dear @crvernon @rmflight @corybrunson, I would like to thank you for your time and effort you put into our submission. Absolutely wonderful process that improved the submission a lot. Thank you so so much!

crvernon commented 3 years ago

@whedon set v1.1.0 as version

whedon commented 3 years ago

OK. v1.1.0 is the version.

crvernon commented 3 years ago

@whedon set 10.5281/zenodo.5517823 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.5517823 is the archive.

crvernon commented 3 years ago

@mingzehuang @muellsen @irinagain - thanks for putting together a really nice software product! Thanks to @rmflight and @corybrunson for a constructive and timely review!

I am recommending that your submission be accepted. An EIC will review this shortly and confirm final publication if all goes well.

crvernon commented 3 years ago

@whedon recommend-accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

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

OK DOIs

- 10.1093/biomet/asaa007 is OK
- 10.1080/00401706.2012.727746 is OK
- 10.1111/rssb.12168 is OK
- 10.1080/10618600.2021.1882468 is OK
- 10.21105/joss.02306 is OK
- 10.3389/fgene.2019.00516 is OK
- 10.1214/12-aos1041 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 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/2598

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2598, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

kthyng commented 3 years ago

Ok everything looks good!

kthyng commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

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

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 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/2599
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03634
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

kthyng commented 3 years ago

Congratulations on your new publication @muellsen! Many thanks to editor @crvernon and reviewers @corybrunson and @rmflight for your time, hard work, and expertise!!

whedon commented 3 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.03634/status.svg)](https://doi.org/10.21105/joss.03634)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03634">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03634/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03634/status.svg
   :target: https://doi.org/10.21105/joss.03634

This is how it will look in your documentation:

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