efficient way to get values from a raster

Dear list,

I want to extract cell values from a raster object given row and column numbers or cell numbers. The solution I used is not efficient (see the following) comparing with extracting values from a matrix. Any advice?

m <- matrix(rnorm(25),5) # matrix
r <- raster(m) # raster

# --- case 1:

system.time(for (i in 1:1000) r[1:3,1:3]) # extracting values from raster given rows and columns

user  system elapsed
      0       0       0

system.time(for (i in 1:1000) m[1:3,1:3])  # extracting the same values from matrix

 user  system elapsed
   8.41    0.03    9.58

I get practically the opposite, which is what I was expecting:

 > m <- matrix(rnorm(25),5) # matrix
 > r <- raster(m) # raster
 > system.time(for (i in 1:1000) r[1:3,1:3])
    user  system elapsed
   3.828   0.176   4.001
 > system.time(for (i in 1:1000) m[1:3,1:3])
    user  system elapsed
   0.004   0.000   0.002

 - much faster for a matrix than a raster. Raster package version: 1.9-94

#---- case 2:

cells <- c(1,2,3,6,7,8,11,12,13) # cell numbers

system.time(for (i in 1:1000) r[cells]) # extracting values from raster given cells number

user  system elapsed
   3.52    0.00    3.59

system.time(for (i in 1:1000) t(m)[cells]) # extracting the same values from matrix

user  system elapsed
   0.07    0.00    0.08

Broadly similar this time:

 > system.time(for (i in 1:1000) r[cells])
    user  system elapsed
   1.436   0.000   1.438
 >  system.time(for (i in 1:1000) t(m)[cells])
    user  system elapsed
    0.04    0.00    0.04

 - matrix faster, as I expected.

 So I guess we now have two questions:

 1. Why is your raster extraction r[1:3,1:3] so much faster than
matrix extraction?
 2. How can you do raster extraction faster?

If this is a real problem in your code (ie extraction is taking >50%
of the time of whatever it is you are doing) then why not convert to
matrix first?

Barry