Dear R-programmer, I wrote an adapted implementation of the Kennard-Stone algorithm for sample selection of multivariate data (R 2.7.1 under MacBook Pro, Processor 2.2 GHz Intel Core 2 Duo, Memory 2 GB 667 MHZ DDR2 SDRAM). I used for the heart of the script three embedded loops. This makes it especially for huge datasets very slow. For a datamatrix of 1853*1853 and the selection of 556 samples needed computation time of more than 24 hours. I did some research on vecotrization, but I could not figure out how to do it better/faster. Which ways are there to replace the time consuming loops?
Here are some information: # val.n<-24; # start.b<-matrix(nrow=1812, ncol=20); # val is a vector of the rownames of 22 in an earlier step chosen extrem samples; # euc<-<-matrix(nrow=1853, ncol=1853); [contains the Euclidean distance calculations] The following calculation of the system.time was for the selection of two samples: system.time(KEN.STO(val.n,start.b,val.start,euc)) user system elapsed 25.294 13.262 38.927 The function: KEN.STO<-function(val.n,start.b,val,euc){ for(k in 1:val.n){ sum.dist<-c(); for(i in 1:length(start.b[,1])){ sum<-c(); for(j in 1:length(val)){ sum[j]<-euc[rownames(start.b)[i],val[j]] } sum.dist[i]<-min(sum); } bla<-rownames(start.b)[which(sum.dist==max(sum.dist))] val<-c(val,bla[1]); start.b<-start.b[-(which(match(rownames(start.b),val[length(val)])! ="NA")),]; if(length(val)>=val.n)break; } return(val); } Regards, Thomas Dr. Thomas Terhoeven-Urselmans Post-Doc Fellow Soil infrared spectroscopy World Agroforestry Center (ICRAF) [[alternative HTML version deleted]] ______________________________________________ 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.