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[REVIEW]: phylogram: an R package for phylogenetic analysis with nested lists #790

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whedon opened this Issue Jun 22, 2018 · 9 comments

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whedon commented Jun 22, 2018

Submitting author: @shaunpwilkinson (Shaun Wilkinson)
Repository: https://github.com/ropensci/phylogram
Version: v2.1.0
Editor: @karthik
Reviewer: @arfon
Archive: 10.5281/zenodo.1293634

Status

status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/6773f7e7465b5068fc5654018c1a33b8"><img src="http://joss.theoj.org/papers/6773f7e7465b5068fc5654018c1a33b8/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/6773f7e7465b5068fc5654018c1a33b8/status.svg)](http://joss.theoj.org/papers/6773f7e7465b5068fc5654018c1a33b8)

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

@arfon, 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 @karthik know.

Review checklist for @arfon

Conflict of interest

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 (v2.1.0)?
  • Authorship: Has the submitting author (@shaunpwilkinson) 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)?
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whedon commented Jun 22, 2018

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @arfon 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:

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
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whedon commented Jun 22, 2018

Attempting PDF compilation. Reticulating splines etc...
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whedon commented Jun 22, 2018

@arfon arfon added the accepted label Jun 22, 2018

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arfon commented Jun 22, 2018

Fast-track accepting because of ropensci/onboarding#212

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arfon commented Jun 22, 2018

@whedon set 10.5281/zenodo.1293634 as archive

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whedon commented Jun 22, 2018

OK. 10.5281/zenodo.1293634 is the archive.

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arfon commented Jun 22, 2018

@shaunpwilkinson - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00790 ⚡️ 🚀 💥

@arfon arfon closed this Jun 22, 2018

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whedon commented Jun 22, 2018

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

If you would like to include a link to your paper from your README use the following code snippet:

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00790/status.svg)](https://doi.org/10.21105/joss.00790)

This is how it will look in your documentation:

DOI

We need your help!

Journal of Open Source Software is a community-run journal and relies upon volunteer effort. If you'd like to support us please consider doing either one (or both) of the the following:

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shaunpwilkinson commented Jun 25, 2018

Thanks so much @arfon and others. What a nice smooth process!

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