[R] lmer for 3-way random anova

[Dick Beyer]

I tried the following on my RedHat EL system:

> lmer(ge~1+(1|trt)+(1|tim)+(1|ctr)+(1|trt:tim)+(1|trt:ctr),data=dat) 
*** glibc detected *** corrupted double-linked list: 0x000000001182d210 *** 
Aborted


> sessionInfo() 
R version 2.2.0, 2005-10-06, x86_64-unknown-linux-gnu

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

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

I will try your suggestion of the experimental version of Matrix next.

Thanks very much for the 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 
http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html 
http://staff.washington.edu/~dbeyer 
*******************************************************************************

On Sat, 10 Dec 2005, Douglas Bates wrote:

> 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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>