Rmarkdown with Rstudio and for all stages of my scientific projects has been a remarkable shift in how my work gets done!
There are so many advantages to this type of workflow, not least of which are reproducibility and transparency (both are crucial for scientists as well as public servants).
I’ve been using this approach as much as possible recently, and I’m quite happy with it.
The entire process can be done using
Rmarkdown etc. but there are still a few challenges which I’ll touch on below.
Is your R script taking too long? Do you find yourself rerunning things over and over? Are you using loops or lapply and think that these are slowing you down? In many cases, working with parallel computing in R can help solves these problems. Working on a super computer with 100s or 1000s of nodes can potentially help a lot.