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

Date: Wed, 30 Apr 2008 17:30:52 -0400

Date: Wed, 30 Apr 2008 17:30:52 -0400

This is the missing Matlab code:

function[fc_matrix]=grw_permute(fc_vector)

fc_matrix(index)=fc_vector(i);

fc_matrix(index+1)=fc_vector(j);

On Wed, Apr 30, 2008 at 4:47 PM, Ray Brownrigg <Ray.Brownrigg_at_mcs.vuw.ac.nz> wrote:

> On Thu, 01 May 2008, 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.
**>
**> I am not a MATLAB user, but I suspect it wasn't "the same code" that
**> produced
**> an answer in MATLAB, but you don't provide your MATLAB code, nor do you
**> specify what version of R, of MATLAB, or what hardware and OS you are
**> using.
**>
**> I get {NetBSD, R version 2.6.0 (2007-10-03), Core 2 Duo, 3.x GHz}:
**> > input_fc <- sample(1:600)
**> > unix.time(a1 <- grw_permute(input_fc))
**> user system elapsed
**> 3.279 -0.001 3.280
**> > unix.time({n <- length(input_fc); a2 <- matrix(c(rep(input_fc, each=n),
**> rep(input_fc, n)), 2, n*n, byrow = T)})
**> user system elapsed
**> 0.019 0.020 0.040
**> > all.equal(a1, a2)
**> [1] TRUE
**> >
**> A sample of length 300 took less than 1 second using your grw_permute()
**> (so
**> your OS may be making a difference as well).
**> >
**> > Am I missing sth in R.. Is there a away to optimize. ???
**> >
**> Yes. Loops are not efficient in R.
**>
**> > Thanks
**>
**> HTH,
**> Ray Brownrigg
**>
*

-- 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 - 21:47:29 GMT

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