lmer for 3-way random anova
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 treated as random. I was wondering if someone could direct me to an example of how to do this using lmer from lme4.
I have 3 main effects, tim, trt, ctr, and all the interaction effects tim*trt*ctr. The response variable is ge.
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" "base"
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
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