On 12-06-24 4:50 PM, Søren Højsgaard wrote:
Dear all,
Indexing matrices from the Matrix package with [i,j] seems to be very slow. For
example:
library(rbenchmark)
library(Matrix)
mm<- matrix(c(1,0,0,0,0,0,0,0), nr=20, nc=20)
MM<- as(mm, "Matrix")
lookup<- function(mat){
for (i in 1:nrow(mat)){
for (j in 1:ncol(mat)){
mat[i,j]
}
}
}
benchmark(lookup(mm), lookup(MM), columns=c("test", "replications", "elapsed",
"relative"), replications=50)
test replications elapsed relative
1 lookup(mm) 50 0.01 1
2 lookup(MM) 50 8.77 877
I would have expected a small overhead when indexing a matrix from the Matrix
package, but this result is really surprising...
Does anybody know if there are faster alternatives to [i,j] ?
There's also a large overhead when indexing a dataframe, though Matrix
appears to be slower. It's designed to work on whole matrices at a
time, not single entries. So I'd suggest that if you need to use [i,j]
indexing, then try to arrange your code to localize the access, and
extract a submatrix as a regular fast matrix first. (Or if it will fit
in memory, convert the whole thing to a matrix just for the access. If
I just add the line
mat <- as.matrix(mat)
at the start of your lookup function, it becomes several hundred times
faster.)
______________________________________________
R-help@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.
