Use Rmarkdown in vignettes

[dan-knight]

The vignettes in BPG use Sweave .Rnw format. This is essentially LaTeX with added support for running chunks of R code - essentially the same as Rmarkdown, just with LaTeX for the main text content rather than Markdown. Further, the R functionality is seemingly identical to Rmd's (including its settings).

While there's nothing wrong with this, I think that the package would benefit from using Rmd format for its vignettes. Rmd has become the standard for R package vignettes and is likely to be prioritized for new features in the future. For example, R packages such as knitr have prioritized support for Rnw. In the lab, I think that the simplicity advantage of Markdown would make contributing to the vignette much more accessible. Further, I don't see anything in the existing vignettes that couldn't be easily achieved with Rmd. We can even keep the visual style of LaTeX when rendering the Rmd document! Rmd also supports LaTeX and HTML chunks, so we can always fall back on that if absolutely necessary.

@pboutros @tyamaguchi-ucla
Is there any context I'm missing from BPG's past? Did we opt to use Sweave over Rmarkdown for any specific technical reason? If so, is it still relevant?