library(raster)
r <- raster(nrow=100, ncol=100)
  r[] <- round(runif(ncell(r),1,4),0)

r1=r; r2=r; r3=r; r4=r # make copies of original to modify
  r1[] <- ifelse(r[] == 1, 1, 0)
  r2[] <- ifelse(r[] == 2, 1, 0)
  r3[] <- ifelse(r[] == 3, 1, 0)
  r4[] <- ifelse(r[] == 4, 1, 0)

plot(stack(r1,r2,r3,r4))

r <- stack(brick(array(runif(100 * 100 * 5), dim=c(100, 100, 5))))
  for(i in 1:nlayers(r)) { r[[i]][] <- round(runif(ncell(r),
                           sample(1:2,1),sample(3:5,1) ),0) }

binary.rasters <- stack()
  for(i in 1:nlayers(r)) {
    for(j in 1:length(unique(r[[i]][]))) {
      u <- unique(r[[i]][])
      b <- r[[i]]
      b[] <- ifelse(b[] == u[j], 1, 0)
      binary.rasters <- addLayer(binary.rasters, b)
    }