Joss-reviews: [REVIEW]: genieR: An R package for inference of demographic history of phylogenies

[whedon]

Submitting author: @xiangfstats (Fei Xiang)
Repository: https://github.com/xiangfstats/GenieR
Version: v1.0.0
Editor: @pjotrp
Reviewer: @pboesu
Archive: 10.5281/zenodo.2532305

Status

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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) 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

@pboesu, please carry out your review in this issue by updating the checklist below. If you cannot edit the checklist please:

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### 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: Does the release version given match the GitHub release (v1.0.0)?
  ⚠️ TODO: No github release exists. DESCRIPTION file lists version as 0.1.0. Please harmonize version numbering and create github release.
• [x] Authorship: Has the submitting author (@xiangfstats) 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?
  Installation works as described on the reviewers machine (Windows 10, R 3.4.2, Rtools 3.5)
  ⚠️ Suggestion: It might be worth pointing out (for the benefit of Windows users - not sure what the target audience is likely using) that a C++ compiler / Rtools installation is necessary. See PR.
• [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?
  ⚠️ Suggestion: Automated tests are provided covering input checking. All of these appear to be 'negative tests' i.e. based on expect_error(). I'd suggest that the authors also implement tests that check the code provides correct output when provided with correct inputs.
• [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?
• [ ] References: Do all archival references that should have a DOI list one (e.g., papers, datasets, software)?

[whedon]

Hello human, I'm @whedon. I'm here to help you with some common editorial tasks. @pboesu it looks like you're currently assigned as the reviewer for 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:

1. 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 :page_facing_up: <--

[george-githinji]

@pboesu how are you getting on with the review process? Kindly let me know if you need some assistance or if you have any concerns. Thank you.

[pboesu]

@biorelated Apologies for being dreadfully slow on the review. I have started it finally, and I hope to finish it by next weekend.

[pboesu]

Hello @biorelated and @xiangfstats

I have reviewed the package now and provided a number of issues in the target repositories that, in my opinion, warrant responses from the authors.

Critically, the vignette does not compile because of an error in one of the package functions (https://github.com/xiangfstats/GenieR/issues/2), but I would also suggest a number of fairly minor changes to the documentation, API, and testing suite that should greatly improve the re-use potential of the package.

[george-githinji]

Thank you very much @pboesu for the review.
@xiangfstats kindly respond to the raised issues.

[xiangfstats]

Dear @george-githinji
I have made improvements based on @pboesu 's suggestions and replied separately to those 7 issues.
Thanks very much for the review from @pboesu .
Best
Fei

[arfon]

:wave: @pboesu - could you take a look at the feedback from @xiangfstats.

[george-githinji]

Dear @pboesu Please review the improvements made by @xiangfstats. Kindly let me know if you need some assistance or if you are not in a position to. Thank you.

[pboesu]

Hi @george-githinji apologies for the slow response, I aim to complete the review this week.

[arfon]

Hi @george-githinji - what's the status of this submission?

[george-githinji]

@pboesu Please were you able to complete this review. unfortunately this has taken longer than expected. If you are not in a position to review. Kindly let me know so that we can assign this to a different reviewer.

[george-githinji]

@arfon I will seek for a new reviewer for this work. @pboesu has not responded to our requests.

[george-githinji]

@whedon list reviewers

[whedon]

Here's the current list of reviewers: https://bit.ly/joss-reviewers

[pjotrp]

@whedon assign @pjotrp as editor

[pjotrp]

Thanks everone. @xiangfstats sorry for the delay and thank you for your interesting contribution. The review process is now complete - I checked the final boxes. To finalize your submission and accept your paper in JOSS, we need two things. First, can you confirm that all references in your bibliography have a DOI (if one exists).

Second, we need you to deposit a copy of your software repository (including any revisions made during the JOSS review process) with a data-archiving service. To do so:

1. Create a GitHub release of the current version of your software repository
2. Deposit that release with Zenodo, figshare, or a similar DOI issuer.
3. Post a comment here with the DOI for the release.

[xiangfstats]

Dear @pjotrp ,
I can confirm that all references have a DOI except two without DOIs. I created a Github release and deposit that release with Zenodo. The DOI is DOI: 10.5281/zenodo.2532305. Many thanks
Best
Fei

[pjotrp]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[pjotrp]

@whedon set 10.5281/zenodo.2532305 as archive

[whedon]

OK. 10.5281/zenodo.2532305 is the archive.

[pjotrp]

Thank you @xiangfstats. Looking good. @arfon, I think we are good to publish. I am trying to tick the DOI checkbox but it won't do it.

[pjotrp]

Oh, it did work. Needed to think about it, I guess ;)

[pjotrp]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/423

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/423, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[pjotrp]

@arfon I guess I should leave this step to you!

[arfon]

@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:

1. Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/424
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.00634
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...

[arfon]

@pboesu - many thanks for your review and to @pjotrp and @george-githinji for editing this submission ✨

@xiangfstats - your paper is now accepted into JOSS :zap::rocket::boom:

[whedon]

: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](http://joss.theoj.org/papers/10.21105/joss.00634/status.svg)](https://doi.org/10.21105/joss.00634)

HTML:
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  <img src="http://joss.theoj.org/papers/10.21105/joss.00634/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.00634/status.svg
   :target: https://doi.org/10.21105/joss.00634

This is how it will look in your documentation:

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[xiangfstats]

Thanks very much to everyone, @arfon, @pboesu, @pjotrp and @george-githinji. Great to know our paper is accepted in JOSS.