Re: [R] lmer for 3-way random anova

From: Dick Beyer <dbeyer_at_u.washington.edu>
Date: Tue 13 Dec 2005 - 04:50:15 EST


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@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
>>
>> ______________________________________________
>> R-help@stat.math.ethz.ch mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide!
http://www.R-project.org/posting-guide.html
>>

>

R-help@stat.math.ethz.ch mailing list
https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Tue Dec 13 05:00:49 2005

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