[R] Code to replace nested for loops

[Liaw, Andy]

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 at nih.gov
> 
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