See
?table
for details.
> tmp <- '       y    x
+ 1      1 2008
+ 2      1 2008
+ 3      0 2008
+ 4      0 2009
+ 5      1 2009'
> data <- read.table(textConnection(tmp), header=TRUE)
> data
  y    x
1 1 2008
2 1 2008
3 0 2008
4 0 2009
5 1 2009
> table(data$x, data$y)
       0 1
  2008 1 2
  2009 1 1
>