neighbours <- array(0, c(100,100))
for (i in 1:100) { neighbours[i,i] = 1 }    #reflexive

> class(neighbours[5])
[1] "numeric"
> class(neighbours[5]) <- "integer"
> class(neighbours[5])
[1] "numeric"

neighbors <- array(FALSE, c(100,100))
diag(neighbors) <- TRUE

> object.size(array(0, c(100,100)))
80200 bytes
> object.size(array(FALSE, c(100,100)))
40200 bytes

m <- matrix(0L, 100, 100)
diag(m) <- 1L

m2 <- diag(1L, 100, 100)

> object.size(m)
40200 bytes
> object.size(m2)
80200 bytes

R> neighbours <- array(0, c(100,100))
R> for (i in 1:100) { neighbours[i,i] = 1 }
R> str(neighbours)
 num [1:100, 1:100] 1 0 0 0 0 0 0 0 0 0 ...
R> storage.mode(neighbours) <- "integer"
R> str(neighbours)
 int [1:100, 1:100] 1 0 0 0 0 0 0 0 0 0 ...
R> storage.mode(neighbours) <- "logical"
R> str(neighbours)
 logi [1:100, 1:100] TRUE FALSE FALSE FALSE FALSE FALSE ...

library(Matrix)
Matrix(diag(1,4) , sparse=TRUE)
#---------
4 x 4 sparse Matrix of class "dsCMatrix"

[1,] 1 . . .
[2,] . 1 . .
[3,] . . 1 .
[4,] . . . 1

> m <- matrix(rnorm(25), 5)
> m[] <- as.integer(m)
# you do need those square-brackets or the structure becomes a dimensionless vector.
> m
     [,1] [,2] [,3] [,4] [,5]
[1,]    0    0   -1    0    0
[2,]    1    0    0    0    0
[3,]    1    0    0    0    0
[4,]    0    0    0    0    0
[5,]    0    0    0   -1    0