[REVIEW]: tacmagic: PET Analysis in R

[whedon]

Submitting author: @eebrown (Eric E. Brown)
Repository: https://github.com/ropensci/tacmagic
Version: v0.2.0
Editor: @danielskatz
Reviewer: @danielskatz
Archive: 10.5281/zenodo.2577947

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/439558885d9eb0b74abb55c0bd556900"><img src="http://joss.theoj.org/papers/439558885d9eb0b74abb55c0bd556900/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/439558885d9eb0b74abb55c0bd556900/status.svg)](http://joss.theoj.org/papers/439558885d9eb0b74abb55c0bd556900)

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) 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

@danielskatz, 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.theoj.org/about#reviewer_guidelines. Any questions/concerns please let @danielskatz know.

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

Review checklist for @danielskatz

Conflict of interest

• 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

• I confirm that I read and will adhere to the JOSS 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?
• Version: Does the release version given match the GitHub release (v0.2.0)?
• Authorship: Has the submitting author (@eebrown) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?

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 function 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

• Authors: Does the paper.md file include a list of authors with their affiliations?
• A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
• References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @danielskatz it looks like you're currently assigned as the reviewer for this paper 🎉.

⭐ 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:

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

For a list of things I can do to help you, just type:

@whedon commands

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

👉 Check article proof 📄 👈

[danielskatz]

This submission has been accepted to rOpenSci. The review thread can be found at ropensci/software-review#280

[danielskatz]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

OK DOIs

- http://doi.org/10.1097/00004647-199609000-00008 is OK
- http://doi.org/10.1001/archneur.65.11.1509 is OK

MISSING DOIs

- https://doi.org/10.1016/j.jalz.2005.06.297 may be missing for title: Simplified quantification of Pittsburgh Compound B amyloid imaging PET studies: a comparative analysis

INVALID DOIs

- None

[danielskatz]

@whedon set 10.5281/zenodo.2577947 as archive

[whedon]

OK. 10.5281/zenodo.2577947 is the archive.

[danielskatz]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

OK DOIs

- http://doi.org/10.1097/00004647-199609000-00008 is OK
- http://doi.org/10.1001/archneur.65.11.1509 is OK

MISSING DOIs

- https://doi.org/10.1016/j.jalz.2005.06.297 may be missing for title: Simplified quantification of Pittsburgh Compound B amyloid imaging PET studies: a comparative analysis

INVALID DOIs

- None

[whedon]

Check final proof 👉 openjournals/joss-papers#525

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#525, 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]

@whedon accept deposit=true

[whedon]

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

[whedon]

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

Here's what you must now do:

0. Check final PDF and Crossref metadata that was deposited 👉 Creating pull request for 10.21105.joss.01281 joss-papers#526
1. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01281
2. If everything looks good, then close this review issue.
3. Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? notify your editorial technical team...

[whedon]

🎉🎉🎉 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](http://joss.theoj.org/papers/10.21105/joss.01281/status.svg)](https://doi.org/10.21105/joss.01281)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01281">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01281/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01281/status.svg
   :target: https://doi.org/10.21105/joss.01281

This is how it will look in your documentation:

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