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signaturescience / skater

SKATE R Utilities
https://signaturescience.github.io/skater/
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Write a paper #48

Closed stephenturner closed 3 years ago

stephenturner commented 3 years ago

Where to submit?

Only reason I'd shoot for Bioinformatics first is that it's indexed in pubmed (JOSS is not). Both are about the same length/content. We could shoot for Bioinformatics, then pivot to JOSS if we get a desk rejection.

Let's write the paper in Rmd in this repo. Couple of ways to handle that:

  1. In an orphan branch that'll never get merged
  2. In a subdirectory added to .Rbuildignore that'll eventually get merged with master.

(See also rticles package has templates for both JOSS and Bioinformatics: https://github.com/rstudio/rticles)

stephenturner commented 3 years ago

Prior art:

stephenturner commented 3 years ago

Note, a few updates to the rticles Bioinformatics template, must be installed via devtools::install_github("rstudio/rticles")

stephenturner commented 3 years ago

hey @vpnagraj I just pushed the formatted paper and supplementary materials compiled from the vignette. See paper/paper.Rmd on the paper branch. Would you take the first review?

paper.pdf

supplement-vignette.pdf

stephenturner commented 3 years ago

Remember you'll need to install rticles from github if you want to compile. Also if you have a better idea for how to do what I'm doing in that first un-echoed un-eval'd chunk in the paper.Rmd, please let me know.

vpnagraj commented 3 years ago

back over to you @stephenturner

edits to wording throughout, and added a couple of references. hopefully got the bibtex formatting correct.

https://github.com/signaturescience/skater/commit/06987b6212ec60ecd994ea3326cd7a76b84fa861

stephenturner commented 3 years ago

Thanks, bibtex worked fine (FWIW, the visual markdown editor citation tool integrates wonderfully with zotero+betterbibtex).

@genignored you're up, please review.

paper.pdf

supplement-vignette.pdf

genignored commented 3 years ago

Not much left to edit. Made a few changes to sentences, otherwise I didn't see anything that needed changes.

Ready to pass to UNT?

stephenturner commented 3 years ago

Thanks @genignored

One thing I should have noted. The supplemental material is derived from the package vignette. Changes you've made to the supplemental will get overwritten with whatever's in the vignette. This is the bit in the paper.Rmd that does that:

https://github.com/signaturescience/skater/blob/f9d111cb6f8b7b2849a74185942c8a898526bbc4/paper/paper.Rmd#L75-L93

It reads in the vignette from skater/vignettes, changes the title in the yaml, writes out to the supplemental Rmd, then renders it into PDF.

Please make the changes to the skater/vignettes/basic_usage.Rmd file, and running that chunk will propagate. Ping back here when done.

genignored commented 3 years ago

updated.