Assume you have suitable "week" indicator and your data is stored in a
data.frame named "data." Then you get the weekly averages by

#simulate data
week <- rep(1:52,each=7)
x <- week+rnorm(52*7,)
y  <- rev(week)+rnorm(52*7)

#create data frame
data=data.frame(week,x,y)

#get weekly averages in a list
averages=unlist(lapply(split(data,week),colMeans))

#unlist averages and store the results in matrix
matrix(averages,byrow=T,ncol=dim(data)[2])

HTH,
Daniel
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