[R] lme : Error in y[revOrder] - Fitted : non-conformable arrays

[Andrew R. Kniss]

Greetings R-helpers,
I am attempting to fit an lme() while specifying a correlation
structure, but I'm getting into trouble long before I get to that point.
I am receiving the error:

Error in y[revOrder] - Fitted : non-conformable arrays

It doesn't seem to matter how simple or complex the model I specify is,
it always gives this same error message.  This makes me suspect
something is wrong with my data set, but I'm not sure where to begin
looking. I can run through the Pinheiro & Bates example on p.240 in a
simplified form, so I know that everything with my installation (R
v2.4.1; nlme v3.1-79; Windows XP) is working fine.  However if I
construct a groupedData object similar in form to the Ovary example, I
will receive the same error, regardless of the model I specify.  I can
plot the groupedData object and get a figure very similar to Fig. 5.10
in Pinheiro & Bates.  I have provided summarized output with a very
simple lme() model, and the exact message.  Any ideas on why the error
is showing up and how I might correct it?

#### Attempting to use my own data ####
> groupedData(CHEAL~rel.year|blk,data=seed.cb[,c(5,1,7)])->cheal.grp
> summary(cheal.grp)
  blk        rel.year     CHEAL      
 I  :36   Min.   :0   Min.   :15.96  
 II :36   1st Qu.:2   1st Qu.:56.70  
 III:36   Median :4   Median :70.76  
 IV :36   Mean   :4   Mean   :68.98  
          3rd Qu.:6   3rd Qu.:82.63  
          Max.   :8   Max.   :99.13  
> lme(CHEAL~rel.year,data=cheal.grp)->cheal.lme
Error in y[revOrder] - Fitted : non-conformable arrays


#### Everything works fine using the Pinheiro & Bates example
#### on page 240 (in a simplified form)
> summary(Ovary)
      Mare          Time           follicles    
 8      : 31   Min.   :-0.1667   Min.   : 1.00  
 4      : 29   1st Qu.: 0.1667   1st Qu.: 8.00  
 5      : 29   Median : 0.5000   Median :12.00  
 1      : 29   Mean   : 0.5000   Mean   :12.04  
 6      : 29   3rd Qu.: 0.8333   3rd Qu.:15.00  
 10     : 29   Max.   : 1.1667   Max.   :25.00  
 (Other):132 
> lme(follicles~Time,data=Ovary)->ovary.lme
> summary(ovary.lme)
Linear mixed-effects model fit by REML
 Data: Ovary 
       AIC      BIC    logLik
  1748.103 1770.445 -868.0515

Random effects:
 Formula: ~Time | Mare
 Structure: General positive-definite
            StdDev   Corr  
(Intercept) 2.682827 (Intr)
Time        3.787545 -0.159
Residual    3.783400       

Fixed effects: follicles ~ Time 
               Value Std.Error  DF   t-value p-value
(Intercept) 10.86191 0.8828363 296 12.303430  0.0000
Time         2.28347 1.2719903 296  1.795194  0.0736
 Correlation: 
     (Intr)
Time -0.27 

Standardized Within-Group Residuals:
        Min          Q1         Med          Q3         Max 
-2.74071048 -0.62051954 -0.05461339  0.70634887  2.70641284 

Number of Observations: 308
Number of Groups: 11 
>




Andrew Kniss
University of Wyoming
Department 3354
1000 E. University Ave.
Laramie WY, 82071

Email:   akniss at uwyo.edu
Office:  (307) 766-3949
Fax:     (307) 766-5549