library(data.table)
dataGenFunc <- function() sample.int(3L, 1e5, TRUE)
DT <- data.table(v1 = dataGenFunc(), v2 = dataGenFunc(), v3 = dataGenFunc())
sampleDT <- rbindlist(lapply(split(DT, by = names(DT)), function(subDT){
  subDT[sample.int(nrow(subDT), round(nrow(subDT)*2/3))]
}))