Joss-reviews: [REVIEW]: blendR: Combining a Probability and a Non-Probability Sample in a Capture-Recapture Setting

[whedon]

Submitting author: @williamsbenjamin (Benjamin Williams)
Repository: https://github.com/williamsbenjamin/blendR
Version: 1.0
Editor: @leeper
Reviewer: @pdwaggoner
Archive: 10.5281/zenodo.1344665

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

@pdwaggoner, 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 @leeper know.

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

Review checklist for @pdwaggoner

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 (1.0)?
• [x] Authorship: Has the submitting author (@williamsbenjamin) 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 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. @pdwaggoner 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: <--

[leeper]

@pdwaggoner The review issue is here. I think you're familiar with the process by now but let me know if you have any questions.

[pdwaggoner]

@leeper Thanks for this. Happy to help. Where is the review issue? (I think its missing the link in your previous message)

[pdwaggoner]

@leeper Apologies; disregard that last message. Figured it out; turns out reading the full page helps... I will get the review back shortly and ping you when I am finished.

[pdwaggoner]

Overall, this looks great. Interesting, simple method. Clearly programmed, and well packaged. I would like to see a couple updates to the paper based on the reviewer guidelines:

1. Example usage: the author does a great job of describing functionality and application of the estimators in the context of fisheries. But the author starts the paper with a broad statement of the (clear) value of sampling in statistical inference, despite the application of the methods focusing quite narrowly. I would like to see even a sentence or two on real world application of the estimators in other non-fisheries contexts.

2. Community guidelines: though its clear anyone can open an issue ticket in GitHub, it wasn't clearly stated in the paper the willingness and options to do so. Just a little more on how to report bugs, options/outlets for outside contributions and so on would be useful given that this is an open source package.

3. Statement of need: I thought the statement of need could be a little clearer and more up front in the manuscript. The value of the method is clear enough, but the need for the package and method got a little lost for me. This point is linked with my comment on example usage above. Again, just a sentence or rewording to make the need perfectly clear would be nice.

Other than that, no major issues. Great work @williamsbenjamin ! Over to you @leeper

[williamsbenjamin]

@pdwaggoner thank you very much! These are great comments and I will fix them up right away. Thank you for your time, it is much appreciated!

@leeper should I go ahead and recompile the pdf after I make the changes?

[williamsbenjamin]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

--> Check article proof :page_facing_up: <--

[williamsbenjamin]

@pdwaggoner I have gone through and changed the paper to reflect the comments you had. Please let me know if you think I should go into more details or fix anything else!

[pdwaggoner]

@williamsbenjamin everything looks great to me! Thanks for making those changes so quickly. And again, great work! Let me know if you need anything else in the meantime.

[williamsbenjamin]

@pdwaggoner Thank you very much!

[leeper]

@williamsbenjamin The review process is now complete. To finalize your submission and accept your paper in JOSS, 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 to @leeper with the DOI for the release.

Let me know if you have any questions about the process.

Oh, and one other really small thing: you'll need to drop the | file LICENSE bit of this: https://github.com/williamsbenjamin/blendR/blob/master/DESCRIPTION#L8 and add LICENSE to an .Rbuildignore file. R CMD check does not allow a LICENSE file for GPL-3.

[williamsbenjamin]

@leeper Great! I have fixed the LICENSE issues. Here is the DOI: 10.5281/zenodo.1344665

Let me know if you need anything else from me!

[leeper]

@whedon set 10.5281/zenodo.1344665 as archive

[whedon]

OK. 10.5281/zenodo.1344665 is the archive.

[leeper]

@arfon over to you

[arfon]

@pdwaggoner - many thanks for your review here and to @leeper for editing this submission ✨

@williamsbenjamin - your paper is now accepted into JOSS and your DOI is https://doi.org/10.21105/joss.00886 :zap: :rocket: :boom:

[whedon]

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

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[williamsbenjamin]

Thank you everyone!