[R-sig-ME] lmer give error message

[array chip]

Hi, I have an ophthalmology dataset, that has as response variable "y", patient 
ID (pid), visit (0,1,2) and eye examined ("L' and "R").

Basically, each patient has 3 visit, during each visit, both eyes will be 
assessed and produce response measurements. The first question is should I treat 
eye.examined and visit as crossed or nested? I think it should be treated as 
crossed because each eye will be assessed in each visit. On the other hand, the 
2 measurements from the 2 eyes were from a given visit, so it looks like it can 
be treated as nested as well (eye %in% visit). 


The second question is, no matter which way I use, lmer() gives me error 
message, while lme() from nlme package can handle nested design easily. Also, is 
there a way to specify corssed design in lme() as well?


> dat <- read.table ("dat.txt", sep='\t', row.names=1, header=T)
> library(nlme)

    ### nested using lme
> lme(y~1, random=~1|pid/visit/eye,dat)
Random effects:
 Formula: ~1 | pid
        (Intercept)
StdDev:    2.881611

 Formula: ~1 | visit %in% pid
        (Intercept)
StdDev:   0.8154632

 Formula: ~1 | eye %in% visit %in% pid
        (Intercept)  Residual
StdDev:    1.065172 0.5321993

    ### nested using lmer
> lmer(y~1+(1|pid/visit/eye),dat)
Error: length(f1) == length(f2) is not TRUE
In addition: Warning messages:
1: In visit:pid :
  numerical expression has 718 elements: only the first used
2: In visit:pid :
  numerical expression has 718 elements: only the first used

    ### crossed 
> lmer(y~1+(1|pid/visit)+(1|pid/eye),dat)
Error: length(f1) == length(f2) is not TRUE
In addition: Warning messages:
1: In visit:pid :
  numerical expression has 718 elements: only the first used
2: In visit:pid :
  numerical expression has 718 elements: only the first used
3: In eye:pid : numerical expression has 718 elements: only the first used
4: In eye:pid : numerical expression has 718 elements: only the first used


Can anyone share their thoughts.

Thanks

John


      
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