... (just a comment)
and since this appears to be O(m^2 x n), where m,n are the number of rows and columns (correction requested if I got this wrong), it would appear that some basically C level functionality -- perhaps the one Jean suggested? -- would be required for even moderately "large" matrices. Cheers, Bert Bert Gunter Genentech Nonclinical Biostatistics (650) 467-7374 "Data is not information. Information is not knowledge. And knowledge is certainly not wisdom." Clifford Stoll On Tue, Jan 20, 2015 at 10:10 AM, Adams, Jean <jvad...@usgs.gov> wrote: > Jorge, > > I have not used it myself, but you might find the dist() function in the > proxy package to be useful. > > http://cran.r-project.org/web/packages/proxy/index.html > > Jean > > On Mon, Jan 19, 2015 at 7:38 AM, Jorge I Velez <jorgeivanve...@gmail.com> > wrote: > >> Dear all, >> >> Given vectors "x" and "y", I would like to compute the proportion of >> entries that are equal, that is, mean(x == y). >> >> Now, suppose I have the following matrix: >> >> n <- 1e2 >> m <- 1e4 >> X <- matrix(sample(0:2, m*n, replace = TRUE), ncol = m) >> >> I am interested in calculating the above proportion for every pairwise >> combination of rows. I came up with the following: >> >> myd <- function(X, p = NROW(X)){ >> D <- matrix(NA, p, p) >> for(i in 1:p) for(j in 1:p) if(i > j) D[i, j] <- mean(X[i, ] == X[j,]) >> D >> } >> >> system.time(d <- myd(X)) >> >> However, in my application n and m are much more larger than in this >> example and the computational time might be an issue. I would very much >> appreciate any suggestions on how to speed the "myd" function. >> >> Note: I have done some experiments with the dist() function and despite >> being much, much, much faster than "myd", none of the default distances >> fits my needs. I would also appreciate any suggestions on how to include >> "my own" distance function in dist(). >> >> Thank you very much for your time. >> >> Best regards, >> Jorge Velez.- >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> 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. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.
