Closed whedon closed 7 years ago
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The authors developed a Ruby package enabling random forest based classification for genomics selection data. The package is well written, quite easy to use and overall it seems a solid piece of software addressing specific analysis using SNPs data. The package is answering all JOSS requirements, although minor revisions are envisaged (marked as checkboxes below).
examples works fine with no errors following Readme instructions and using the example data provided into the repository
[ ] automated tests fail, an issue has been opened on the repository to inspect this
[ ] The paper describes clearly the background of random forests algorithm and the use of Nimbus, but the statements of need could be improved by describing what Nimbus adds to existing random forest classifiers available for genomics selection, and highlighting what are the strong points of Nimbus and the reason why it was developed (e.g. simplicity to use, better fit for specific use cases, better performance etc.)
[ ] Minor grammar and typing errors (can be easily spotted using a word processor, Markdown isn't very helpful with this)
@fstrozzi thanks for your thorough review! @xuanxu looks like these are minor fixes. Ping us when you are done or respond here.
Thanks for the review @fstrozzi!
I've add some details to the paper summary to highlight the strong points and improve the statement of need. And also corrected some typos.
Hi @xuanxu, the new version of the paper.md looks good (only a couple of typos left, in the second paragraph "accomodate" should be "accommodate" and in the very last line "use" should be "used"). I have also closed the issue on the repository since after the last exchanges we had, the tests run fine also on my end now.
@pjotrp from my point of view all the points raised were addressed.
Nice! Both typos fixed.
@arfon we are ready!
@xuanxu - At this point could you make an archive of the reviewed software in Zenodo/figshare/other service and update this thread with the DOI of the archive? I can then move forward with accepting the submission.
@arfon - Done: DOI: 10.5281/zenodo.845342
@whedon set 10.5281/zenodo.845342 as archive
OK. 10.5281/zenodo.845342 is the archive.
@fstrozzi - many thanks for your review and to @pjotrp for editing this submission ✨
@xuanxu - your paper is now accepted into JOSS and your DOI is http://dx.doi.org/10.21105/joss.00351 ⚡️ 🚀 💥
Yay! Thank you @fstrozzi, @pjotrp & @arfon 🎉
Submitting author: @xuanxu (Juanjo Bazán) Repository: https://github.com/xuanxu/nimbus Version: 2.3.0 Editor: @pjotrp Reviewer: @fstrozzi Archive: 10.5281/zenodo.845342
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