Joss-reviews: [REVIEW]: bbsAssistant: An R package for downloading and handling data and information from the North American Breeding Bird Survey.

[whedon]

Submitting author: @trashbirdecology (Jessica Burnett)
Repository: https://github.com/TrashBirdEcology/bbsAssistant/
Version: v1.0
Editor: @kthyng
Reviewer: @ethanwhite , @jsta
Archive: 10.5066/P93W0EAW

Status

Status badge code:

HTML: <a href="https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69"><img src="https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69/status.svg"></a>
Markdown: [![status](https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69/status.svg)](https://joss.theoj.org/papers/4b445373a7a7806c92e17bdd194a8e69)

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

@ethanwhite & @jsta , 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 @kthyng know.

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

Review checklist for @ethanwhite

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@trashbirdecology) 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?
• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

Review checklist for @jsta

Conflict of interest

• [x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

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] Contribution and authorship: Has the submitting author (@trashbirdecology) 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?
• [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 functionality 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] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
• [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] State of the field: Do the authors describe how this software compares to other commonly-used packages?
• [x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
• [x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

[whedon]

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

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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]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kthyng]

@ethanwhite Will you be able to work on your review soon?

[ethanwhite]

Apologies for they delay. I have it on my high priority list for this week.

[kthyng]

@ethanwhite Just a friendly ping here.

[ethanwhite]

Thanks @kthyng and apologies again. Hoping to get this done very soon.

[ethanwhite]

I've completed my checklist level review. Below are sections related to fixes for boxes that I haven't checked yet:

Automated tests

• Two tests are currently failing in my local build for test-get_regions.R, but they seem to be passing on Travis so maybe I have a missing dependency or something. Ubuntu 18.04, R 3.6.1.

Community Guidelines

• Contributing and CoC links were broken. Fixed in https://github.com/TrashBirdEcology/bbsAssistant/pull/65
• No clear description of how to "Report issues or problems with software" or "Seek support". There is some language related to reporting issues in
  CONTRIBUTING.md.

State of the field

There are two additional packages that contain some of the functionality described here:

1. rBBS - This package is acknowledged as a source of some code, but no comparison is made to it in the paper.
2. rdataretriever (software by my group) - which downloads BBS and loads it into R. This package works on the entire integrated BBS dataset, does not support data manipulation, and does not work with the BBS analyses, so there are definitely meaningful differences from this package and therefore no conflict with publishing this software paper. However, it does have some meaningful overlap and so may be worth mentioning here. It is potentially a useful alternative for users looking to work with a full integrated version of the BBS data.

References

• The rBBS package should be cited.
• If rdataretriever is added then it and the associated retriever package (https://doi.org/10.21105/joss.00451)

I have some additional suggestions related to the functionality of the package and the API, but those are out of scope for the JOSS review checklist so I will open them as issues over in the bbsAssistant repository. (I will try to remember to tag this issue in case there is interest in considering them as part of this review).

[kthyng]

Hi @TrashBirdEcology! Just want to make sure you saw that @ethanwhite has some recommendations for you for moving forward.

[trashbirdecology]

@ethanwhite @jsta - we have addressed the unchecked boxes in your reviews (see below).

We have done some major re-writing of code in /R/, which I hope makes the top-level functioning more intuitive. This is outlined in the quick overview vignette.

We have also addressed the issues you opened in the repository, with the exception of adding mapping features (a feature request by @jsta).

@ethanwhite

• Community guidelines enhanced by adding a CONTRIBUTING.md and codeofconduct.md. Will be pushed to master upon resubmission.
• Tests were updated. Happy to receive suggestions for improving testing.

@ethanwhite and @jsta

• A section, State of the Field, and better reference to the relevant packages have been added to the paper.md, and will be regenerated.

We appreciate the time you have already taken to provide critical feedback on this package -- it has been greatly improved.

[ethanwhite]

@TrashBirdEcology - apologies for the difficulties with rdataretriever (don't see them in this issue any more, but got a email notification about them). The retriculate package that we rely on for talking to Python has introduced a number of bugs and we're in the midst of trying to mitigate these issues through improved installation instructions until they get them fixed. You current mention of this and other associated packages is all that's needed here.

@TrashBirdEcology @kthyng - these changes all look great and I very much appreciate the productive engagement both on these issues and suggestions related to design! It's been a pleasure working with you both. I've completed the rest of the check boxes and consider this software paper ready for publication.

[trashbirdecology]

Thanks, @ethanwhite!

I removed the comment as I wasn't sure whether it was an issue with my PC +Py. Wanted to test on multiple machines before issuing

[jsta]

Looks good to me. The issues I raised with the initial review have all been addressed. Only thing I see remaining is that the paper still mentions the feather file format even though this functionality has been removed?

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[trashbirdecology]

Yikes -- I guess I didn't push that edit.

This has been resolved @jsta.

Jessica L. Burnett

GitHub http://github.com/trashbirdecology
CV/Resume
https://github.com/TrashBirdEcology/cv/blob/master/burnett_extendedCV.pdf
ORC ID: 0000-0002-0896-5099 https://orcid.org/0000-0002-0896-5099

On Tue, Nov 26, 2019 at 10:04 AM Joseph Stachelek [e-mail]
wrote:

Looks good to me. The issues I raised with the initial review have all
been addressed. Only thing I see remaining is that the paper still mentions
the feather file format even though this functionality has been removed?

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[whedon]

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

[kthyng]

Great! I see the go-ahead from @ethanwhite.

@jsta can you confirm that the recent change has resolved your last concern?

[jsta]

Looks good. :+1:

[kthyng]

Great! We can begin the final acceptance process then.

[kthyng]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kthyng]

I read through the paper and made a few small fixed in this PR if you want to merge.

[kthyng]

@whedon check references

[whedon]

Attempting to check references...

[whedon]

```Reference check summary:

OK DOIs

• 10.1650/CONDOR-17-83.1 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[kthyng]

Forgot to look through your references before I made that PR so here is another: https://github.com/TrashBirdEcology/bbsAssistant/pull/86

[kthyng]

@TrashBirdEcology Can you make a tagged release and archive, and report the version number and archive DOI in this review thread?

[kthyng]

Sorry I should have been more specific, by "archive" I mean to submit your JOSS submission to Zenodo or similar for a DOI.

[trashbirdecology]

@kthyng, yes, I will archive on USGS, but that might take a few days. I will ping you as soon as this is complete.

[kthyng]

When you archive with USGS will it be the code and paper like you would with Zenodo? And you get a DOI?

Also in case it was lost in the mix, please do make a tagged release and we'll set that as the new version. Your original version number is ok but it should match a tagged release in github.

[trashbirdecology]

Yes, similar to Zenodo, including a DOI.

Not sure what is meant by 'tagged' release, however?

Jessica L. Burnett

GitHub http://github.com/trashbirdecology
CV/Resume
https://github.com/TrashBirdEcology/cv/blob/master/burnett_extendedCV.pdf
ORC ID: 0000-0002-0896-5099 https://orcid.org/0000-0002-0896-5099

On Mon, Dec 2, 2019 at 8:15 AM Kristen Thyng [e-mail]
wrote:

When you archive with USGS will it be the code and paper like you would
with Zenodo? And you get a DOI?

Also in case it was lost in the mix, please do make a tagged release and
we'll set that as the new version. Your original version number is ok but
it should match a tagged release in github.

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[kthyng]

@TrashBirdEcology I'm following editor guidelines here: https://joss.readthedocs.io/en/latest/editing.html#after-reviewers-recommend-acceptance

And here is some information about making releases in github: https://help.github.com/en/github/administering-a-repository/creating-releases

[kthyng]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[kthyng]

@TrashBirdEcology Looks like the changes to the references haven't made it through?

[trashbirdecology]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

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

[trashbirdecology]

@kthyng the changes should be updated.

__DOI__ for V1.0 software: 10.5066/P93W0EAW
__Version release__: https://github.com/TrashBirdEcology/bbsAssistant/releases/tag/v1.0

[kthyng]

@whedon set v1.0 as version

[whedon]

OK. v1.0 is the version.

[kthyng]

@whedon set 10.5066/P93W0EAW as archive

[whedon]

OK. 10.5066/P93W0EAW is the archive.

[kthyng]

@TrashBirdEcology I'm not familiar with this archive setup. Normally with Zenodo I would go to the website of your submission there and make sure the title and author list match your paper. Can you do that for your archive?

[trashbirdecology]

@kthyng I apologies for being a difficult customer here, but I am not sure what you mean by this? The DOI archive (https://doi.org/10.5066/P93W0EAW) contains a .zip file of the V1.0 release instance of the package.

[kthyng]

@TrashBirdEcology You're not being difficult at all! I see at your archive link now that your title and author list is consistent with your JOSS submission. I wanted to check that since it isn't always true.

[kthyng]

@whedon accept

[whedon]

Attempting dry run of processing paper acceptance...

[whedon]

```Reference check summary:

OK DOIs

• 10.1650/CONDOR-17-83.1 is OK

MISSING DOIs

• None

INVALID DOIs

• None
  ```

[whedon]

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/1152

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/1152, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.
@whedon accept deposit=true

[kthyng]

@whedon accept deposit=true

[whedon]

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

[whedon]

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

[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/1153
2. Wait a couple of minutes to verify that the paper DOI resolves https://doi.org/10.21105/joss.01768
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...

[trashbirdecology]

Ahh yes I see you referred to the title and authorship discrepancies. Apologies!!

Sent from my iPhone

On Dec 4, 2019, at 7:50 AM, Kristen Thyng [e-mail] wrote:


@TrashBirdEcology You're not being difficult at all! I see at your archive link now that your title and author list is consistent with your JOSS submission. I wanted to check that since it isn't always true.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub, or unsubscribe.

[kthyng]

Congratulations on your new paper @TrashBirdEcology!!! Many thanks to reviewers @ethanwhite and @jsta for your time and expertise.

[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:

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reStructuredText:
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[trashbirdecology]

Congratulations on your new paper @TrashBirdEcology!!! Many thanks to reviewers @ethanwhite and @jsta for your time and expertise.

thank you for handling @kthyng