Re: [R] do faster ANOVAS

[melissa]

Thank you, with the matrix for the responses (here my 101 timepoints), it takes 
less than 30 minutes for 1000 pemutations, whereas before it takes 2h30!

Best regards,

Mélissa





> Message du 10/06/10 18:52
> De : "Douglas Bates" 
> A : "melissa" 
> Copie à : r-help@r-project.org
> Objet : Re: [R] do faster ANOVAS
> 
> 
> The lm and aov functions can take a matrix response allowing you to
> fit all of the responses for a single attribute simultaneously.
> 
> 
> On Thu, Jun 10, 2010 at 8:47 AM, melissa wrote:
> > Dear all R users,
> > I want to realize 800 000 ANOVAS and to store Sum of Squares of the 
> > effects. Here is an extract of my table data
> > Product attribute subject rep t1 t2 t3 … t101
> > P1 A1 S1 R1 1 0 0 … 1
> > I want to realize 1 ANOVA per timepoint and per attribute, there are 101 
> > timepoints and 8 attributes so I want to realize 808 ANOVAS. This will be 
> > an ANOVA with two factors :
> > Here is one example:
> > Aov(t1~Subject*Product,data[data$attribute==”A1”,])
> > I want to store for each ANOVA SSprod,SSsujet,SSerreur,SSinter and SStotal.
> > In fact I want the result in several matrices:
> > Ssprod matrice:
> > T1 t2 t3 t4 … t101
> > A1 ssprod(A1,T1)
> > A2
> > A3
> > …
> > A8
> > So I would like a matrice like that for ssprod, ssujet,sserreur,ssinter and 
> > sstotal.
> > And this is for one permutation, and I want to do 1000 permutations
> > Here is my code:
> > SSmatrixglobal<-function(k){
> >
> > daten.temp<-data
> > daten.temp$product=permutations[[k]]
> > listmat<-apply(daten.temp[,5:105],2,function(x,y){
> > tab2<-as.data.frame(cbind(x,y))
> > tab.class<-by(tab2[,1:3],tab2[,4],function(x){
> > f <- formula(paste(names(x)[1],"~",names(x)[2],"*",names(x)[3],sep=""))
> > anovas <- aov(f, data=x)
> > anovas$call$formula <-f
> > s1 <- summary(anovas)
> > qa <- s1[[1]][,2]
> > return(qa)
> > })
> > return(tab.class)
> > },y=daten.temp[,1:3]
> > )
> > ar <- 
> > array(unlist(listmat),dim=c(length(listmat[[1]][[1]]),length(listmat[[1]]),length(listmat)))
> > l=lapply(1:4,function(i) ar[i,,])
> > sssujet=l[[1]]
> > ssprod=l[[2]]
> > ssinter=l[[3]]
> > sserreur=l[[4]]
> > ss=rbind(sssujet,ssprod,ssinter,sserreur,sstotal)
> > ss=as.data.frame(ss)
> > sqlSave(channel,ss,"SS1000",append=T)
> > rm(ss,numperm,daten.temp)
> > }
> >
> > system.time(por <- lapply(c(1:1000), SSmatrixglobal))
> >
> > But it takes time about 90seconds for a permutation so *1000, how can I do 
> > in order to do faster ANOVAS?
> >
> > Many thanks
> > Best regards
> > Mélissa
> >
> > PS: I think that I can gain a lot of time in the aov function but I don't 
> > know how to do
> > [[alternative HTML version deleted]]
> >
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
> >
> 
>
        [[alternative HTML version deleted]]


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