From: bogdan romocea <br44114_at_gmail.com>

Date: Fri 02 Jun 2006 - 04:29:39 EST

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jun 02 07:58:44 2006

Date: Fri 02 Jun 2006 - 04:29:39 EST

Compare

system.time({

v <- vector()

for (i in 1:10^5) v <- c(v,1)

})

with

system.time({

v <- vector(length=10^5)

for (i in 1:10^5) v[i] <- 1

})

If you don't know exactly how long v will be, use a value that's large
enough, then throw away what's extra.

> -----Original Message-----

*> From: r-help-bounces@stat.math.ethz.ch
**> [mailto:r-help-bounces@stat.math.ethz.ch] On Behalf Of Tim Alcon
**> Sent: Thursday, June 01, 2006 2:04 PM
**> To: r-help@stat.math.ethz.ch
**> Subject: [R] progressive slowdown during script execution?
**>
**> I'm an R novice, so I hope my question is a valid one. I'm trying to
**> run the following script in the current version of R.
**>
**> for (i in 1:1640){for (j in (i+1):1641){
**> if (i == 1 && j == 2){x <-
**> cor(sage[i,],sage[j,],method="spearman"); y
**> <- cor(frie[i,],frie[j,],method="spearman")}
**> if (i != 1 || j != 2){x <-
**> c(x,cor(sage[i,],sage[j,],method="spearman")); y <-
**> c(y,cor(frie[i,],frie[j,],method="spearman"))}}}
**>
**> It basically just finds all pairwise correlations of the rows in a
**> matrix for each of two matrices and stores the results for
**> each matrix
**> in a vector. The problem I seem to be running into is that
**> it seems to
**> slow way down during execution somehow. When I first tried
**> running it I
**> stopped execution to see how fast it was running, before trying to
**> compute the whole job (the two matrices each have 1641 rows).
**> Based on
**> what I saw, I figured it would easily finish overnight.
**> Instead, it was
**> still running almost 24 hours later. To quantify this a
**> little better I
**> checked it after running for 5 minutes, at which point it had added
**> 79120 correlations to each of the x and y vectors. Since
**> there should
**> be a total of (1641*1640)/2 = 1345620 pairwise correlations in each
**> vector when it finishes running, I worked out that it should take
**> (1345620/79120)*5 = 85 minutes to run the whole job. However, when I
**> checked it after running for 2 hours, it had added only 341870
**> correlations to each vector.
**>
**> Any ideas what I'm doing wrong, or why it would run more slowly the
**> longer it runs? Thanks for any help or advice.
**>
**> Tim
**>
**> ______________________________________________
**> R-help@stat.math.ethz.ch mailing list
**> https://stat.ethz.ch/mailman/listinfo/r-help
**> PLEASE do read the posting guide!
**> http://www.R-project.org/posting-guide.html
**>
*

R-help@stat.math.ethz.ch mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Fri Jun 02 07:58:44 2006

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