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[REVIEW]: hypr: An R package for hypothesis-driven contrast coding #2134

Closed whedon closed 4 years ago

whedon commented 4 years ago

Submitting author: @mmrabe (Maximilian Rabe) Repository: https://github.com/mmrabe/hypr Version: v0.1.7 Editor: @marcosvital Reviewer: @tomfaulkenberry, @JonathanReardon Archive: 10.5281/zenodo.3765843

Status

status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/866129b28b619712fa28bbc10bef37c6"><img src="https://joss.theoj.org/papers/866129b28b619712fa28bbc10bef37c6/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/866129b28b619712fa28bbc10bef37c6/status.svg)](https://joss.theoj.org/papers/866129b28b619712fa28bbc10bef37c6)

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

@tomfaulkenberry & @JonathanReardon, 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 @marcosvital know.

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

Review checklist for @tomfaulkenberry

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

Review checklist for @JonathanReardon

Conflict of interest

Code of Conduct

General checks

Functionality

Documentation

Software paper

whedon commented 4 years ago

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

:star: Important :star:

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 commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1016/j.jml.2019.104038 is OK

MISSING DOIs

- None

INVALID DOIs

- None
whedon commented 4 years ago

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

marcosvital commented 4 years ago

Dear @tomfaulkenberry and @JonathanReardon, thank you very much for accepting review this submission for JOSS.

Please check the instructions and checklists above, and let me know if you need any assistance. You can also tag @mmrabe if you need to ask specific questions about the submission.

JonathanReardon commented 4 years ago

Hello, I can't seem to access the checklist at all (unable to tick any boxes), could you look into this for me? apologies if it's a fault my end.

marcosvital commented 4 years ago

Hi, @JonathanReardon, no need to apologize!

In order to be able to tick the boxes, you need to accept the invite as a collaborator on the joss-reviews repository - GitHub should have sent you an invite. This is easily missed depending on how you handle notifications from GitHub, so I'll send you another one.

@whedon re-invite @JonathanReardon as reviewer

Let me know if this works, ok?

JonathanReardon commented 4 years ago

Thanks @marcosvital, I see the invite at the top (I missed that before), though I think it has now expired.

"Sorry, we couldn't find that repository invitation. It is possible that the invitation was revoked or that you are not logged into the invited account"

Could you reset that perhaps? I didn't get any email with an invite, I just noticed the invite at the top of this page.

marcosvital commented 4 years ago

Yes, I can try to reset it, the command I gave Whedon should have done the trick, but I think it didn't work. I'll try again:

marcosvital commented 4 years ago

@whedon re-invite @JonathanReardon as reviewer

whedon commented 4 years ago

Sorry, I couldn't re-invite @jonathanreardon.

marcosvital commented 4 years ago

Didn't work... I'll ask for help with the editor team and will come back here soon, ok?

danielskatz commented 4 years ago

👋 @openjournals/dev - another case where this doesn't seem to work

danielskatz commented 4 years ago

And @marcosvital - FYI, any command to @whedon has to be the start of a comment, not later in the comment (but this isn't the main problem here)

marcosvital commented 4 years ago

And @marcosvital - FYI, any command to @whedon has to be the start of a comment, not later in the comment (but this isn't the main problem here)

Thanks, @danielskatz! I imagined that after my first attempt, as Whedon didn't respond anything.

JonathanReardon commented 4 years ago

All good now, I got the invite! Thank you @marcosvital and @danielskatz

arfon commented 4 years ago

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

tomfaulkenberry commented 4 years ago

I have (finally) completed my review of this paper/package. It is a very nice package, and will be immediately useful as a tool for psychologists who want to translate the (sometimes unfamiliar) R method of specifying contrasts to the way that we are usually taught to specify contrasts.

I left two boxes unchecked in my review above, but I don't think they warrant making new issues on the repo. They are: (1) there is no license in the Github repo, and (2) there is no statement of how people can contribute.

These should be easy to fix.

Functionally, the package installed easily (even on my half-broken installation of R), and the functions did exactly what they were supposed to.

Overall, nice package, and good paper.

Tom

JonathanReardon commented 4 years ago

I too have now finished the review, apologies for the delay, and thank you to all for being understanding. This was a very simple tool to install and use, it worked exactly as intended and behaved exactly as described. No issues at all.

If you could include a license and a brief statement as to how others can contribute to the project, that would be great. I (and @tomfaulkenberry) could then tick off the remaining 2 boxes.

Nice paper and useful tool that I am sure many psychologists would be interested in using.

Thanks all, Jonathan

mmrabe commented 4 years ago

@tomfaulkenberry and @JonathanReardon, thank you both very much for taking the time to review the package and paper and of course for your wonderful feedback! @marcosvital, I hope it’s okay that I went ahead and made the changes to the repository.

I added a “Community guidelines” paragraph to the end of the README file and a LICENSE file (GPL-3) to the root directory. Some of these details can also be found in the DESCRIPTION meta file.

This was a great experience so far and I really enjoyed the interaction. I’m looking forward to hearing from you again.

Thanks a lot and stay safe! Max

tomfaulkenberry commented 4 years ago

Great..thanks @mmrabe! I have finished the checkmarks on my part, and I'm perfectly happy with the final result.

JonathanReardon commented 4 years ago

Thank you @mmrabe, and congrats on the project! Just ticked off the final two boxes, cheers all.

marcosvital commented 4 years ago

Hi, @mmrabe! Sorry about the delayed reply. Since all the reviewers are satisfied, we can carry on.

@JonathanReardon and @tomfaulkenberry , thank you very much for the time and effort put into this review!

@mmrabe, I'll trigger a DOI checking, so we can see if there are any corrections to be done on the references, ok?

marcosvital commented 4 years ago

@whedon check references

whedon commented 4 years ago 
Reference check summary:

OK DOIs

- 10.1016/j.jml.2019.104038 is OK

MISSING DOIs

- None

INVALID DOIs

- None
marcosvital commented 4 years ago

@whedon generate pdf

whedon commented 4 years ago

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

marcosvital commented 4 years ago

@mmrabe, everything is ok with cited DOIs.

I generated a new proof, so you can take a carefull (maybe final?) look at the manuscript. I'll read it myself too, and will let you know if I find any issues, ok?

mmrabe commented 4 years ago

@marcosvital, thank you very much! Sorry for the late response. My coauthors and I have had another look at the manuscript and have found no further issues.

marcosvital commented 4 years ago

Hi, @mmrabe! Sorry about the late reply. Let's move on, everything looks fine with the manuscript.

As one of our last steps, if you already didn't do this, you will need to archive the last release of the package (on Zenodo, figshare, or other of your choice). After that, post the version number and archive DOI here, and we can continue.

mmrabe commented 4 years ago

Hi @marcosvital! Thanks! I just archived the package using Zenodo. The current version number is v0.1.7 (was v0.1.6 upon submission) and the Zenodo DOI is: 10.5281/zenodo.3765843

marcosvital commented 4 years ago

@whedon set 10.5281/zenodo.3765843 as archive

whedon commented 4 years ago

OK. 10.5281/zenodo.3765843 is the archive.

marcosvital commented 4 years ago

@whedon set v0.1.7 as version

whedon commented 4 years ago

OK. v0.1.7 is the version.

marcosvital 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

- 10.1016/j.jml.2019.104038 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/1434

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1434, 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 4 years ago

Thanks - I'll take this from here

danielskatz commented 4 years ago

👋 @mmrabe - please update the metadata in the Zenodo archive, specifically the title, to match the JOSS paper

mmrabe commented 4 years ago

Thanks for pointing that out, @danielskatz. I have now updated the title in Zenodo.

danielskatz 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:

  1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/1435
  2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.02134
  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 commented 4 years ago

We're now waiting for the DOI to work - everything else seems ok

danielskatz commented 4 years ago

Thanks to @tomfaulkenberry & @JonathanReardon for reviewing, and @marcosvital for editing!

And congratulations to @mmrabe (Maximilian Rabe) and co-authors!!

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.02134/status.svg)](https://doi.org/10.21105/joss.02134)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.02134">
  <img src="https://joss.theoj.org/papers/10.21105/joss.02134/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.02134/status.svg
   :target: https://doi.org/10.21105/joss.02134

This is how it will look in your documentation:

DOI

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