[R-sig-ME] crossed effects with lmer but correlation structure with lme

[Denis Vile]

Dear R users,

I'm trying to fit a crossed-effects mixed model that would include a 
spatial correlation structure..
The data come from four controlled experiments (control, treatment1, 
treatment2, treatment1+treatment2) on plants grown in a growth chamber.  
Individual replicates of different genotypes were grown together and 
response traits were measured. A covariate X is included in the model 
with a quadratic form.

We fitted the following model using lmer:

fm1 <- lmer(Y ~ 1 + Trt1*Trt2*poly(X, degree=2, raw=T) +
(1|idGenotype) + (1|Trt2:idGenotype) + (1|Trt1:idGenotype) +
             (1|Trt1:Trt2:idGenotype), data=...)

This model is very interesting because we can extract the BLUPs for each 
genotype in each (crossed) environment.

After discussion with colleagues, it appeared that we should try to 
include the possible spatial heterogeneityof the micro-environmentwithin 
the growth chamber. To this end, we tried to fit a model with lme() 
because we cannot easily (if possible) include a correlation structure 
using lmer(). The model is:

fm2 <- lme(Y ~ (X+I(X^2))*idCondition,
             random =~1|idGenotype/idCondition,
             correlation=corGaus(c(15,0.95), 
form=~x+y|idGenotype/idCondition, nugget=T),
             data =...)

where x and y are the coordinates of the plants within the growth chamber.

Since I was unable to fit the crossed effects Trt1 x Trt2 in lme() I 
coded a new variable idCondition which is the combination of Trt1 and 
Trt2, and treated genotypes within idCondition. This is not entirely 
satisfying because it is impossible to extract all BLUPs as in fm1.

Could you please tell me if I missed something and ifthere is a trick to 
specify crossed effects using lme()?
I assume that this should use pdClasses but I'm not at all at ease with 
the matrix specification of mixed models.
Alternatively, include a correlation structure in lmer seems to be 
unfeasible, am I wrong?

Thank you very much for your help,

Denis


-- 

*Denis VILE*
Chargé de Recherche
Laboratoire d'Ecophysiologie des Plantes sous Stress Environnementaux 
(*LEPSE*)
UMR 759 *INRA*-SUPAGRO // Institut de Biologie Intégrative des Plantes 
(IBIP, bât 7)
2 place Pierre Viala
34060 Montpellier Cedex 2
Tel +33 (0)4 99 61 31 87
Fax +33 (0)4 67 52 21 16
http://www1.montpellier.inra.fr/ibip/lepse/