[R] Why R is 200 times slower than Matlab ?

[Peter Dalgaard]

Zhandong Liu wrote:
> I am switching from Matlab to R, but I found that R is 200 times slower than
> matlab.
>
> Since I am newbie to R, I must be missing some important programming tips.
>
> Please help me out on this.
>
> Here is the function:
> ## make the full pair-wise permutation of a vector
> ## input_fc=c(1,2,3);
> ## output_fc=(
> 1 1 1 2 2 2 3 3 3
> 1 2 3 1 2 3 1 2 3
> );
>
> grw_permute = function(input_fc){
>
> fc_vector = input_fc
>
> index = 1
>
> k = length(fc_vector)
>
> fc_matrix = matrix(0,2,k^2)
>
> for(i in 1:k){
>
> for(j in 1:k){
>
> fc_matrix[index]  =  fc_vector[i]
>
> fc_matrix[index+1]  =  fc_vector[j]
>
> index = index+2
>
> }
>
> }
>
> return(fc_matrix)
>
> }
>
> For an input vector of size 300. It took R 2.17 seconds to run.
>
> But the same code in matlab only needs 0.01 seconds to run.
>
> Am I missing sth in R.. Is there a away to optimize.  ???
>
> Thanks
>
>   
This is pretty characteristic. With R, you really don't want nested 
loops doing single-element accessing (if you have better things to do 
with 2.16 seconds of our life). You will usually find that this sort of 
problem is handled either using vectorized operations at a higher level, 
or pushed into C code which is dynamically loaded. For the particular 
problem, notice that the same result is obtained with

 > system.time(rbind(rep(1:300,300),rep(1:300,each=300)))
   user  system elapsed
  0.041   0.006   0.050

or even (OK, so it's transposed)

 > system.time(expand.grid(1:300,1:300))
   user  system elapsed
  0.027   0.011   0.040


-- 
   O__  ---- Peter Dalgaard             Øster Farimagsgade 5, Entr.B
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