How about this:

ddply(test.set, .(site), colwise(max))
On Wednesday, May 11, 2011 at 11:46 AM, Justin wrote: 
> test.set<-data.frame(site=1:10,x=.Random.seed[1:100],y=rnorm(100))
> means<-ddply(test.set,.(site),mean)
> means 


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