From: Zhandong Liu <zhandong_at_mail.med.upenn.edu>

Date: Wed, 30 Apr 2008 16:15:46 -0400

1 1 1 2 2 2 3 3 3

1 2 3 1 2 3 1 2 3

);

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.

## 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 [[alternative HTML version deleted]] ______________________________________________ R-help_at_r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.Received on Wed 30 Apr 2008 - 20:22:10 GMT

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