accelerating code execution in R to provide counting of all possible combinations of events belonging to certain ID

Question

I have a data set that has 3 columns , (ID , D , AE).

sample=data.frame(
ID=c(1,1,1,2,2,2),
  D=c(\'a\',\'b\',\'c\',\'a\',\'c\',\'c\'),
  AE=c(\'m\',\'x\',\'w\',\