[REVIEW]: molic: An R package for multivariate outlier detection in contingency tables

whedon commented 5 years ago

Submitting author: @mlindsk (Mads Lindskou) Repository: https://github.com/mlindsk/molic Version: v1.0.0 Editor: @csoneson Reviewer: @jdeligt, @jkanche Archive: 10.5281/zenodo.3475854

Status

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Markdown: [![status](https://joss.theoj.org/papers/9fa65ced7bf3db01343d68b4488196d8/status.svg)](https://joss.theoj.org/papers/9fa65ced7bf3db01343d68b4488196d8)

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

@jdeligt & @jkanche, 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 @csoneson know.

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

Review checklist for @jdeligt

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v1.0.0
[x] Authorship: Has the submitting author (@mlindsk) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

Review checklist for @jkanche

Conflict of interest

[x] As the reviewer I confirm that I have read the JOSS conflict of interest policy and that there are no conflicts of interest for me to review this work.

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] Version: v1.0.0
[x] Authorship: Has the submitting author (@mlindsk) 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 function 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] Authors: Does the paper.md file include a list of authors with their affiliations?
[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] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

whedon commented 5 years ago

Attempting to check references...

whedon commented 5 years ago


OK DOIs

- 10.1111/sjos.12407 is OK
- 10.1038/nature15393 is OK
- 10.1016/j.tpb.2017.12.004 is OK
- 10.1016/j.fsigen.2014.06.014 is OK

MISSING DOIs

- None

INVALID DOIs

- None

csoneson commented 5 years ago

@mlindsk - I noticed one more typo in the paper: first sentence of the use case should be "advances [...] have", not "advances [...] has". Could you fix this and generate a new pdf proof (@whedon generate pdf)?

The next steps are then as follows:

[ ] Check that the software version is consistently reported
[ ] Create a tagged release of the current version of the software and report the version tag here
[ ] Archive the software in Zenodo. Make sure that the title and authors of the archive are the same as those of the paper (you can also add ORCID)
[ ] Report back the doi of the Zenodo archive here

mlindsk commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

mlindsk commented 5 years ago

@csoneson

Tag: v1.0.0
DOI: 10.5281/zenodo.3475854

csoneson commented 5 years ago

@mlindsk Please fix the metadata of the Zenodo archive - the title and authors should be the same as the paper.

mlindsk commented 5 years ago

@mlindsk Please fix the metadata of the Zenodo archive - the title and authors should be the same as the paper.

@csoneson I was a little too fast I see; should be fixed now.

csoneson commented 5 years ago

I still see the title "mlindsk/molic: First release", and authors "mlindsk; Charlotte Soneson" on the DOI above.

mlindsk commented 5 years ago

Ok - I was not aware that I should hit "publish" after saving.

csoneson commented 5 years ago

@whedon set 10.5281/zenodo.3475854 as archive

whedon commented 5 years ago

OK. 10.5281/zenodo.3475854 is the archive.

csoneson commented 5 years ago

@whedon set v1.0.0 as version

whedon commented 5 years ago

OK. v1.0.0 is the version.

csoneson commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.1111/sjos.12407 is OK
- 10.1038/nature15393 is OK
- 10.1016/j.tpb.2017.12.004 is OK
- 10.1016/j.fsigen.2014.06.014 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1008

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1008, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

csoneson commented 5 years ago

@mlindsk - ok, looks good! I'll hand over to @openjournals/joss-eics to finalize the process

mlindsk commented 5 years ago

@csoneson

Thank you very much for all the work you have put into this project - it is very much appreciated for a first-timer like me!

labarba commented 5 years ago

The acronym SNP is used without ever spelling it out. (Of course, also DNA, but this being of popular knowledge, it can pass.)

labarba commented 5 years ago

@mlindsk 👋 — I am the Associate Editor-in-Chief on rotation this week. Will you add the meaning of the acronym SNP to the paper before we publish?

mlindsk commented 5 years ago

@whedon generate pdf

whedon commented 5 years ago

Attempting PDF compilation. Reticulating splines etc...

whedon commented 5 years ago

:point_right: Check article proof :page_facing_up: :point_left:

mlindsk commented 5 years ago

Hi @labarba The meaning of the SNP acronym is now added.

labarba commented 5 years ago

@whedon accept

whedon commented 5 years ago

Attempting dry run of processing paper acceptance...

whedon commented 5 years ago


OK DOIs

- 10.1111/sjos.12407 is OK
- 10.1038/nature15393 is OK
- 10.1016/j.tpb.2017.12.004 is OK
- 10.1016/j.fsigen.2014.06.014 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 5 years ago

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1019

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1019, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

whedon commented 5 years ago

I'm sorry @mlindsk, I'm afraid I can't do that. That's something only editor-in-chiefs are allowed to do.

labarba commented 5 years ago

@whedon accept deposit=true

whedon commented 5 years ago

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

whedon commented 5 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 5 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/1020
Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01665
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

labarba commented 5 years ago

Congratulations, @mlindsk, your JOSS paper is published! 🚀

Huge thanks to our editor: @csoneson, and the reviewers: @jdeligt, @jkanche — your contribution to JOSS is greatly appreciated! 🙏

whedon commented 5 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.01665/status.svg)](https://doi.org/10.21105/joss.01665)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01665">
  <img src="https://joss.theoj.org/papers/10.21105/joss.01665/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.01665/status.svg
   :target: https://doi.org/10.21105/joss.01665

This is how it will look in your documentation:

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