Creating a sequence in a data.table depending on a column

Here is an option:

set.seed(1)
DT <- data.table(R=sample(0:1, 10000, rep=TRUE), Seq=0L)
DT[, Seq:=seq(.N), by=list(cumsum(c(0, abs(diff(R)))))]
DT

We create a counter that increments every time your 0-1 variable changes using cumsum(abs(diff(R))). The c(0, part is to ensure we get the correct length vector. Then we split by it with by. This produces:

       R Seq
    1: 0   1
    2: 0   2
    3: 1   1
    4: 1   2
    5: 0   1
   ---      
 9996: 1   1
 9997: 0   1
 9998: 1   1
 9999: 1   2
10000: 1   3

---

EDIT: Addressing request for clarification:

lets look at the computation I'm using in by, broken down into two new columns:

DT[, diff:=c(0, diff(R))]
DT[, cumsum:=cumsum(abs(diff))]
print(DT, topn=10)

Produces:

       R Seq diff cumsum
    1: 0   1    0      0
    2: 0   2    0      0
    3: 1   1    1      1
    4: 1   2    0      1
    5: 0   1   -1      2
    6: 1   1    1      3
    7: 1   2    0      3
    8: 1   3    0      3
    9: 1   4    0      3
   10: 0   1   -1      4
   ---                  
 9991: 1   2    0   5021
 9992: 1   3    0   5021
 9993: 1   4    0   5021
 9994: 1   5    0   5021
 9995: 0   1   -1   5022
 9996: 1   1    1   5023
 9997: 0   1   -1   5024
 9998: 1   1    1   5025
 9999: 1   2    0   5025
10000: 1   3    0   5025

You can see how the cumulative sum of the absolute of the diff increments by one each time R changes. We can then use that cumsum column to break up the data.table into chunks, and for each chunk, generate a sequence using seq(.N) that counts to the number of items in the chunk (.N represents exactly that, how many items in each by group).