Joss-reviews: [REVIEW]: portalr: an R package for summarizing and using the Portal Project Data

[whedon]

Submitting author: @emchristensen (Erica Christensen)
Repository: https://github.com/weecology/portalr
Version: v0.1.4
Editor: @karthik
Reviewer: @Pakillo
Archive: 10.5281/zenodo.2546883

Status

Status badge code:

HTML: <a href="http://joss.theoj.org/papers/d985813ed51d34bc7f54da1b0253c7ec"><img src="http://joss.theoj.org/papers/d985813ed51d34bc7f54da1b0253c7ec/status.svg"></a>
Markdown: [![status](http://joss.theoj.org/papers/d985813ed51d34bc7f54da1b0253c7ec/status.svg)](http://joss.theoj.org/papers/d985813ed51d34bc7f54da1b0253c7ec)

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

@Pakillo, 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.

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

Review checklist for @Pakillo

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 (v0.1.4)?
• [x] Authorship: Has the submitting author (@emchristensen) 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?
• [ ] 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]

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @Pakillo 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]

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

[karthik]

Noting here that @Pakillo will take an additional two weeks since he is quite busy with his own deadlines.

[Pakillo]

Hi there,

Thanks for inviting me to review portalr. I have been playing with the package and it works nicely! The work you are doing to manage and facilitate reuse and sharing of data from the Portal Project is really impressive. Leading by example.

I only had a few minor comments or suggested changes.

I have opened a few issues in the original repo (https://github.com/weecology/portalr/issues/created_by/Pakillo), most of them just suggestions to consider, and have submitted a couple of pull requests (https://github.com/weecology/portalr/pull/177 & https://github.com/weecology/portalr/pull/178) with very minor fixes for one vignette.

I think some functions would benefit from a somewhat more developed documentation (e.g. specify output values, add examples, improve descriptions of expected parameters...). But I understand that takes time, and at least all the functions I tried seem to work well.

The only item I could not yet check from the review checklist above is that of having DOIs for all references. I have requested them to be added (https://github.com/weecology/portalr/issues/179). Once this is done I am happy to recommend publication!

[emchristensen]

Hi @Pakillo ,
Thank you for the review, and all your suggestions! We added DOIs for the references (weecology/portalr#183), and did some re-factoring of the load_functions (weecology/portalr#187) to make function names more consistent and descriptive. I can't promise we've added a significant amount of documentation as of now, but it's something we can work on as the package grows, and we will certainly keep it in mind.

Thanks again for your suggestions, and let us know if there are any other changes you would like to see.

[Pakillo]

Hi @emchristensen et al.

Thanks for considering my suggestions. It's all fine from my side. I've completed checklist above. @karthik please let me know if there's something else I should do

Cheers

[karthik]

Thanks very much @Pakillo
@emchristensen if you can now archive this on Zenodo and provide a DOI, I can proceed with the next steps. 🙏

[karthik]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[emchristensen]

Proofs look good. DOI for the package is 10.5281/zenodo.2546883

Is there anything else we need to do?

[karthik]

@whedon set 10.5281/zenodo.2546883 as archive

[whedon]

OK. 10.5281/zenodo.2546883 is the archive.

[karthik]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/453

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/453, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[karthik]

@whedon accept deposit=true

[whedon]

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

[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/454
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01098
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]

@Pakillo - many thanks for your review and to @karthik for editing this submission ✨

@emchristensen - 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.01098/status.svg)](https://doi.org/10.21105/joss.01098)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.01098">
  <img src="http://joss.theoj.org/papers/10.21105/joss.01098/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: http://joss.theoj.org/papers/10.21105/joss.01098/status.svg
   :target: https://doi.org/10.21105/joss.01098

This is how it will look in your documentation:

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