R help - May 2003 - lme speedup question

I am hoping someone will be kind enough to have a look at the following piece of
code and tell me if there is a way to run lme() so it is a lot faster. The inner
loop, j in 1:15000, takes about 2 hrs on my 2.8GHz dual Xeon 4GB RAM machine. 
The timings I have done show the dominant execution time is in lme.

options(contrasts=c("contr.sum", "contr.sum"))
getOption("contrasts")
vg  <- c(1,2,1,2,2,1,2,1,1,2,1,2,2,1,2,1,1,2,1,2,2,1,2,1)
ag  <- c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,6,6,6,6)
dy  <- c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2)
rp  <- c(1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3)

for (perm in 1:216){
 vg <- vgAll[perm,]
 for(j in 1:15000){
  ge <- c(philmaanova.rloess$adjdata[j,1:24])
  dat <-
data.frame(ge,vg=factor(vg),ag=factor(ag),dy=factor(dy),rp=factor(rp))
  dat$vgrp <- getGroups(dat, form = ~ 1|vg/rp, level = 2)
  ge.lme   <- lme(fixed=ge~vg+ag+dy, data=dat, random=~1|vgrp)
  cp1[j,1] <- philmaanova.rloess$cloneid[j]
  tmpInt   <- intervals(ge.lme,level=0.95,which="fixed")
  cp1[j,2] <- tmpInt$fixed[2,2]*2
  cp1[j,3] <- tmpInt$fixed[2,1]
  cp1[j,4] <- tmpInt$fixed[2,3]
}
}

An Aside: I am using lme for a mixed model with treating rp as random and nested
in the fixed effect vg.  I am collecting the coefficients and se's so I can
later calculate a modified t-test (like SAM does, Significance Analysis of
Microarrays).

Thanks very much for any help,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099

Thanks very much to the help I received on my lme speedup question.  Jake Bowers
pointed out that memory fill might slow things down, so I will keep watch on
that.  Renaud Lancelot pointed out using update instead of redoing lme in the
inner loop (also to look at using gls as it might be faster).  That sped up
things by about 9%.  Douglas Bates pointed out my unnecessary creation of
structures in the inner loop, so I moved the creation of the data.frame to the
outermost loop.  With these changes, I see about a 27% speedup, for which I am
very grateful.

My modified code 

for (perm in 1:216){
  vg <- vgAll[perm,]
  ge <- c(philmaanova.rloess$adjdata[1,1:24])
  dat <-
data.frame(ge,vg=factor(vg),ag=factor(ag),dy=factor(dy),rp=factor(rp))
  dat$vgrp <- getGroups(dat, form = ~ 1|vg/rp, level = 2)
  ge.lme   <- lme(fixed=ge~vg+ag+dy, data=dat, random=~1|vgrp)

  for(j in 1:15000){
    dat$ge   <- c(philmaanova.rloess$adjdata[j,1:24])
    ge.lme   <- update(ge.lme, data=dat)
    cp1[j,1] <- philmaanova.rloess$cloneid[j]
    tmpInt   <- intervals(ge.lme,level=0.95,which="fixed")
    cp1[j,2] <- tmpInt$fixed[2,2]*2
    cp1[j,3] <- tmpInt$fixed[2,1]
    cp1[j,4] <- tmpInt$fixed[2,3]
  }
}
> I am hoping someone will be kind enough to have a look at the following
piece
of code and tell me if there is a way to run lme() so it is a lot faster. The
inner loop, j in 1:15000, takes about 2 hrs on my 2.8GHz dual Xeon 4GB RAM
machine.  The timings I have done show the dominant execution time is in
lme.
> 
> options(contrasts=c("contr.sum", "contr.sum"))
> getOption("contrasts")
> vg  <- c(1,2,1,2,2,1,2,1,1,2,1,2,2,1,2,1,1,2,1,2,2,1,2,1)
> ag  <- c(1,1,1,1,2,2,2,2,3,3,3,3,4,4,4,4,5,5,5,5,6,6,6,6)
> dy  <- c(1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2,1,2)
> rp  <- c(1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,3,3,3,3,3,3,3,3)
> 
> for (perm in 1:216){
>  vg <- vgAll[perm,]
>  for(j in 1:15000){
>   ge <- c(philmaanova.rloess$adjdata[j,1:24])
>   dat <-
data.frame(ge,vg=factor(vg),ag=factor(ag),dy=factor(dy),rp=factor(rp))
>   dat$vgrp <- getGroups(dat, form = ~ 1|vg/rp, level = 2)
>   ge.lme   <- lme(fixed=ge~vg+ag+dy, data=dat, random=~1|vgrp)
>   cp1[j,1] <- philmaanova.rloess$cloneid[j]
>   tmpInt   <- intervals(ge.lme,level=0.95,which="fixed")
>   cp1[j,2] <- tmpInt$fixed[2,2]*2
>   cp1[j,3] <- tmpInt$fixed[2,1]
>   cp1[j,4] <- tmpInt$fixed[2,3]
> }
> }
Thanks for all your help,
Dick
*******************************************************************************
Richard P. Beyer, Ph.D.	University of Washington
Tel.:(206) 616 7378	Env. & Occ. Health Sci. , Box 354695
Fax: (206) 685 4696	4225 Roosevelt Way NE, # 100
			Seattle, WA 98105-6099