RE: [R] Code to replace nested for loops

From: Liaw, Andy <andy_liaw_at_merck.com>
Date: Thu 17 Mar 2005 - 10:30:49 EST


You may be able to simplify it further, but just by replacing the whole inner-most loop with

      opt.mat2[k,j] <- mean(x.mat[kt == x.mat[, nc], j])

the computation is instantaneous on my 1.6GHz Pentium M laptop (whereas your code took just over 7 seconds).

HTH,
Andy

> From: Haynes, Maurice (NIH/NICHD)
>
> Dear list members,
>
> How can I replace the nested for loops at then end of the script
> below with more efficient code?
>
> # Begin script__________________________________________________
> # Dichotomous scores for 100 respondents on 3 items with
> # probabilities of a correct response = .6, .4, and .7,
> # respectively
> x1 <- rbinom(100,1,.6)
> x2 <- rbinom(100,1,.4)
> x3 <- rbinom(100,1,.7)
>
> # 'theta.vec' is a vector holding 31 possible levels of theta
> # ranging from -3 to +3 in intervals of .2.
> theta.vec <- seq(-3,3,.2)
> theta <- sample(rep(theta.vec,5),100)
> x.mat <- (cbind(x1,x2,x3,theta))
> rm(x1,x2,x3,theta)
>
> nc <- ncol(x.mat)
> ni <- nc - 1
> nr <- nrow(x.mat)
> ntheta <- length(theta.vec)
>
> # 'opt.mat' is a matrix which will hold the observed proportions
> # correct at each level of theta for each item. Rows have
> # dimnames corresponding to the 31 levels of theta and columns
> # have dimnames corresponding to the item names.
> opt.mat <- matrix(rep(NA,ni*ntheta),nrow=ntheta, ncol=ni,
> dimnames=list(round(theta.vec,1),c(dimnames(x.mat)[[2]][1:ni])))
>
> # Set of nested for-loops to compute the observed proportions
> # correct at each level of theta for each item and store them in
> # the appropriate row and column locations of the 'opt.mat'.
> system.time(
> for(j in 1:ni)
> {for (k in 1:ntheta) {
> n.theta.cat <- 0
> sum.theta.cat <- 0
> kt <- theta.vec[k]
> for(i in 1:nr) {
> it <- x.mat[i,nc]
> if(identical(all.equal(kt,it),TRUE)) n.theta.cat
> <- n.theta.cat
> + 1
> if(identical(all.equal(kt,it),TRUE)) sum.theta.cat <-
> sum.theta.cat + x.mat[i,j]
> if(n.theta.cat > 0) opt.mat[k,j] <- sum.theta.cat
> / n.theta.cat
> }
> }
> }
> )
> # End script____________________________________________________
>
> On my Dell 863 MHz machine with 512 MB RAM running Windows XP SP2,
> the loop to 21 sec to execute.
>
> Thanks,
>
> Maurice Haynes
> National Institute of Child Health and Human Development
> Child and Family Research Section
> 6705 Rockledge Drive, Suite 8030
> Bethesda, MD 20892
> Voice: 301-496-8180
> Fax: 301-496-2766
> E-Mail: mh192j@nih.gov
>
> ______________________________________________
> 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 Thu Mar 17 10:39:19 2005

This archive was generated by hypermail 2.1.8 : Fri 03 Mar 2006 - 03:30:50 EST