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

From: Zhandong Liu <zhandong_at_mail.med.upenn.edu>
Date: Wed, 30 Apr 2008 16:15:46 -0400


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

-- 
Zhandong Liu

Genomics and Computational Biology
University of Pennsylvania

616 BRB II/III, 421 Curie Boulevard
University of Pennsylvania School of Medicine
Philadelphia, PA 19104-6160

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