I would use matrix indexing. From ?"["
:
A third form of indexing is via a numeric matrix with the one column for each dimension: each row of the index matrix then selects a single element of the array, and the result is a vector.
Making use of that nice feature:
my.matrix <- matrix(0, nrow=length(region), ncol=length(unique(region)))
my.matrix[cbind(seq_along(region), region)] <- 1
# [,1] [,2] [,3]
# [1,] 1 0 0
# [2,] 1 0 0
# [3,] 1 0 0
# [4,] 1 0 0
# [5,] 1 0 0
# [6,] 1 0 0
# [7,] 0 1 0
# [8,] 0 1 0
# [9,] 0 1 0
# [10,] 0 0 1
# [11,] 0 0 1
# [12,] 0 0 1
# [13,] 0 0 1