The biggest "gotcha" for learning R as a programmer is that R interprets character vectors of data frames as factor vectors by default , which will usually break something in your code. If you're learning R, learn to use dplyr for data manipulation and ggplot2 for plotting. Both will save you a lot of time.
I had been learning data.table, but I really like dplyr's % operator and the compositional functions better. I think I'm going to make the move to dplyr.