Loop in C to make RScript more efficient performance - c

Question

I am trying to compute the number of pairwise differences between each row in a table of 100 rows x 2500 Columns.
I have a small RScript that does this but the run time is (obviously) extremely high!
I am trying to write a loop in C but I keep getting errors (compileCode).
Do you have any idea of how I can "convert" the following loop to C?
pw.dist <- function (vec1, vec2) {
return( length(which(vec1!=vec2)) )
}
N.row <- dim(table)[1]
pw.dist.table <- array( dim = c(dim(table)[1], dim(table)[1]))
for (i in 1:N.row) {
for (j in 1:N.row) {
pw.dist.table[i,j] <- pw.dist(table[i,-c(1)], table[j,-c(1)])
}
}
I am trying something like:
sig <- signature(N.row="integer", table="integer", pw.dist.table="integer")
code <- "
for( int i = 0; i < (*N.row) - 1; i++ ) {
for( int j = i + 1; j < *N.row; j++ ) {
int pw.dist.table = table[j] - table[i];
}
}
"
f <- cfunction( sig, code, convention=".C" )
I am a complete newbie when it comes to programming!
Thanks in advance.
JMFA

Answer 1

Before trying to optimize the code,
it is always a good idea to check where the time is spent.
Rprof()
... # Your loops
Rprof(NULL)
summaryRprof()
In your case, the loop is not slow, but your distance function is.
$by.total
total.time total.pct self.time self.pct
"pw.dist" 37.98 98.85 0.54 1.41
"which" 37.44 97.45 34.02 88.55
"!=" 3.12 8.12 3.12 8.12
You can rewite it as follows (it takes 1 second).
# Sample data
n <- 100
k <- 2500
d <- matrix(sample(1:10, n*k, replace=TRUE), nr=n, nc=k)
# Function to compute the number of differences
f <- function(i,j) sum(d[i,]!=d[j,])
# You could use a loop, instead of outer,
# it should not make a big difference.
d2 <- outer( 1:n, 1:n, Vectorize(f) )

Answer 2

Vincent above has the right idea. In addition, you can take advantage of how matrices work in R and get even faster results:
n <- 100
k <- 2500
d <- matrix(sample(1:10, n*k, replace=TRUE), nr=n, nc=k)
system.time(d2 <- outer( 1:n, 1:n, Vectorize(f) ))
#precompute transpose of matrix - you can just replace
#dt with t(d) if you want to avoid this
system.time(dt <- t(d))
system.time(sapply(1:n, function(i) colSums( dt[,i] != dt)))
Output:
#> system.time(d2 <- outer( 1:n, 1:n, Vectorize(f) ))
# user system elapsed
# 0.4 0.0 0.4
#> system.time(dt <- t(d))
# user system elapsed
# 0 0 0
#> system.time(sapply(1:n, function(i) colSums( dt[,i] != dt)))
# user system elapsed
# 0.08 0.00 0.08