[R] help with script

[JOHN VOIKLIS]

Hello,

I wrote the function, below, in the hope of _quickly_ generating a
sliding-window time series of the mean, sd, median, and mad values
from a matrix of data. The script below is anything but quick; it has
been working away on a 2500 x 2500 matrix with a sliding window of 100
x 100 for five days, with no end in sight. Obviously, I am not the
best of programmers. Can anyone offer suggestions as to how I might
optimize this script.

Thank you,

John

common.ground<-function(inMatrix,window){
	
	cleanMatrix<-as.matrix(inMatrix)
	diag(cleanMatrix)<-NA
	outMatrix<-matrix(0,dim(inMatrix)[1]-window,4)
	colnames(outMatrix)<-c("mean","SD", "median","mad")
	
	for(i in 1:dim(outMatrix)[1]){
		for(j in window:dim(cleanMatrix)[2]){
			outMatrix[i,1]<-mean(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
			outMatrix[i,2]<-sd(c(cleanMatrix[c(i:j),c(i:j)]),na.rm=TRUE)
			outMatrix[i,3]<-median(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
			outMatrix[i,4]<-mad(cleanMatrix[c(i:j),c(i:j)],na.rm=TRUE)
		}
	}
	return(outMatrix)
}