[R] Trying to make a nested lme analysis

[Ronaldo Reis Jr.]

Hi,

I'm trying to understand the lme output and procedure.
I'm using the Crawley's book.

I'm try to analyse the rats example take from Sokal and Rohlf (1995).
I make a nested analysis using aov following the book.

> summary(rats)
    Glycogen       Treatment      Rat          Liver  
 Min.   :125.0   Min.   :1   Min.   :1.0   Min.   :1  
 1st Qu.:135.8   1st Qu.:1   1st Qu.:1.0   1st Qu.:1  
 Median :141.0   Median :2   Median :1.5   Median :2  
 Mean   :142.2   Mean   :2   Mean   :1.5   Mean   :2  
 3rd Qu.:150.0   3rd Qu.:3   3rd Qu.:2.0   3rd Qu.:3  
 Max.   :162.0   Max.   :3   Max.   :2.0   Max.   :3  

> attach(rats)
> Treatment <- factor(Treatment)
> Rat <- factor(Rat)
> Liver <- factor(Liver)

> model <- aov(Glycogen~Treatment/Rat/Liver+Error(Treatment/Rat/Liver))
> summary(model)

Error: Treatment
          Df  Sum Sq Mean Sq
Treatment  2 1557.56  778.78

Error: Treatment:Rat
              Df Sum Sq Mean Sq
Treatment:Rat  3 797.67  265.89

Error: Treatment:Rat:Liver
                    Df Sum Sq Mean Sq
Treatment:Rat:Liver 12  594.0    49.5

Error: Within
          Df Sum Sq Mean Sq F value Pr(>F)
Residuals 18 381.00   21.17               
> 

OK,

Then I try to make this analysis using lme.

> model <- lme(Glycogen~Treatment, random=~1|Treatment/Rat/Liver)
> summary(model)
Linear mixed-effects model fit by REML
 Data: NULL 
       AIC      BIC    logLik
  233.6213 244.0968 -109.8106

Random effects:
 Formula: ~1 | Treatment
        (Intercept)
StdDev:    3.541272

 Formula: ~1 | Rat %in% Treatment
        (Intercept)
StdDev:     6.00658

 Formula: ~1 | Liver %in% Rat %in% Treatment
        (Intercept) Residual
StdDev:    3.764883 4.600247

Fixed effects: Glycogen ~ Treatment 
Error in if (any(wchLv <- (as.double(levels(xtTab[, wchPval])) == 0))) { : 
	missing value where logical needed
In addition: Warning message: 
NaNs produced in: pt(q, df, lower.tail, log.p) 
> 

The random effects are correct, the variance component is OK:

In nested aov | In nested lme
Residual
21.1666       | 21.16227
Liver in Rats
14.16667      | 14.17434
Rats in Treatment
36.0648       | 36.079

But I not understand why the Fixed effects error?

What is the problem in my formula to make this analysis using lme?

Thanks for all
Inte
Ronaldo
-- 
Anger kills as surely as the other vices.
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