lmer for 3-way random anova

lmer(ge~1+(1|trt)+(1|tim)+(1|ctr)+(1|trt:tim)+(1|trt:ctr),data=dat) 

sessionInfo() 

If you are running on a Linux system you can try an experimental 
version of the Matrix package that is available from the SVN archive. 
The URL is 

https://svn.r-project.org/R-packages/branches/Matrix-mer2 

The code in that branch uses what is called a supernodal sparse 
Cholesky factorization which works very well for these types of 
models.  Once I get the Laplace and AGQ methods for generalized linear 
mixed models working in this formulation I will merge the branch back 
in to the trunk and release a version of the Matrix package using 
this. 

I haven't created a Windows binary for this experimental branch 
because I still can't get the compilation system to work on my Windows 
computer.  If someone wants to try compiling on Windows from the SVN 
sources I would appreciate it. 

On 12/9/05, Dick Beyer <dbeyer at u.washington.edu> wrote: 

I have been using lme from nlme to do a 3-way anova with all the effects 

I have 3 main effects, tim, trt, ctr,  and all the interaction effects 

Here is my lme code: 


   dat <- data.frame(ge=ge,trt=factor(trt),tim=factor(tim),ctr=factor(ctr)) 
   dat$grp = as.factor(rep(1, nrow(dat))) 

# dim(dat) = 216x5 

   w <- lme(ge ~ 1,data=dat, 
   random = list( 
   grp = pdBlocked(list(  pdIdent(~ trt - 1) 
                         ,pdIdent(~ tim - 1) 
                         ,pdIdent(~ ctr - 1) 
                         ,pdIdent(~ trt:tim - 1) 
                         ,pdIdent(~ trt:ctr - 1) 
                         ,pdIdent(~ tim:ctr - 1) 
                         ,pdIdent(~ trt:tim:ctr - 1) 
                        ) 
                  ) 
                ) 
              ) 

I was trying the following as a starting place: 

   lmer(ge~1+(1|tim)+(1|trt)+(1|ctr), data=dat) 

but this causes my R session to terminate. 

sessionInfo() 

R version 2.2.0, 2005-11-15, i386-pc-mingw32 

attached base packages: 
[1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"  

other attached packages: 
      lme4   lattice    Matrix 
  "0.98-1" "0.12-11"  "0.99-2" 

Thanks very much for any help or pointers, 
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 
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html 
http://staff.washington.edu/~dbeyer