[R-sig-ME] glmer with/without intercept gave different results

[ONKELINX, Thierry]

Dear Ruby,

The hypotheses of those models are different. Hence the diference in
p-values.

Fit1:
H0: Capsule 1 = 0
H0: Capsule 2 - Capsule 1 = 0
H0: Control - Capsule 1 = 0

Fit2:
H0: Capsule 1 = 0
H0: Capsule 2 = 0
H0: Control = 0

However, the predictions of both model should be the same.

Best regards,

Thierry


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek
team Biometrie & Kwaliteitszorg
Gaverstraat 4
9500 Geraardsbergen
Belgium

Research Institute for Nature and Forest
team Biometrics & Quality Assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium

tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
  

> -----Oorspronkelijk bericht-----
> Van: r-sig-mixed-models-bounces at r-project.org 
> [mailto:r-sig-mixed-models-bounces at r-project.org] Namens Chang, Yu-Mei
> Verzonden: donderdag 18 november 2010 15:22
> Aan: r-sig-mixed-models at r-project.org
> Onderwerp: [R-sig-ME] glmer with/without intercept gave 
> different results
> 
> Dear all,
> 
>  
> 
> I have fitted two glmer models (with or without intercept 
> term). I thought the results should be similar if not 
> identical, but they are quite different. I suspect it's 
> related to the random effects. Any suggestions on how to 
> proceed is greatly appreciated.
> 
>  
> 
> Kind regards,
> 
> Ruby Chang
> 
>  
> 
> fit1 <- glmer(Cyptoplasmic.vacuolation ~ Group +  (1|Villus) 
> + (1|Cell),family=binomial(link = "logit"))
> 
> fit2 <- glmer(Cyptoplasmic.vacuolation ~ Group -1 +  
> (1|Villus) + (1|Cell),family=binomial(link = "logit"))
> 
>  
> 
> > table(Cyptoplasmic.vacuolation, Group)
> 
>                         Group
> 
> Cyptoplasmic.vacuolation Capsule 1 Capsule 2 Control
> 
>                        0       560       340    1230
> 
>                        1       190       160      20
> 
>  
> 
> > fit1 <- glmer(Cyptoplasmic.vacuolation ~ Group +  (1|Villus) +
> (1|Cell),family=binomial(link = "logit"))
> 
> > summary(fit1)
> 
> Generalized linear mixed model fit by the Laplace approximation 
> 
> Formula: Cyptoplasmic.vacuolation ~ Group + (1 | Villus) + (1 | Cell) 
> 
>    AIC   BIC logLik deviance
> 
>  138.9 168.1 -64.47    128.9
> 
> Random effects:
> 
>  Groups Name        Variance  Std.Dev.
> 
>  Cell   (Intercept) 1983.5708 44.5373 
> 
>  Villus (Intercept)    5.9475  2.4387 
> 
> Number of obs: 2500, groups: Cell, 250; Villus, 50
> 
>  
> 
> Fixed effects:
> 
>                Estimate Std. Error z value Pr(>|z|)
> 
> (Intercept)     -11.945      9.123  -1.309    0.190
> 
> GroupCapsule 2   -1.409     14.343  -0.098    0.922
> 
> GroupControl    -17.792     33.251  -0.535    0.593
> 
>  
> 
> Correlation of Fixed Effects:
> 
>             (Intr) GrpCp2
> 
> GroupCapsl2 -0.636       
> 
> GroupContrl -0.274  0.175
> 
> > fit2 <- glmer(Cyptoplasmic.vacuolation ~ Group -1 +  (1|Villus) +
> (1|Cell),family=binomial(link = "logit"))
> 
> > summary(fit2)
> 
> Generalized linear mixed model fit by the Laplace approximation 
> 
> Formula: Cyptoplasmic.vacuolation ~ Group - 1 + (1 | Villus) + (1 |
> Cell) 
> 
>    AIC   BIC logLik deviance
> 
>  132.9 162.0 -61.43    122.9
> 
> Random effects:
> 
>  Groups Name        Variance   Std.Dev.  
> 
>  Cell   (Intercept) 5.9933e+03 7.7417e+01
> 
>  Villus (Intercept) 1.2025e-07 3.4677e-04
> 
> Number of obs: 2500, groups: Cell, 250; Villus, 50
> 
>  
> 
> Fixed effects:
> 
>                Estimate Std. Error z value Pr(>|z|)
> 
> GroupCapsule 1   -15.08      17.70  -0.852    0.394
> 
> GroupCapsule 2   -14.72      19.29  -0.763    0.445
> 
> GroupControl     -18.23      54.54  -0.334    0.738
> 
>  
> 
> Correlation of Fixed Effects:
> 
>             GrpCp1 GrpCp2
> 
> GroupCapsl2 0.000        
> 
> GroupContrl 0.000  0.000
> 
> 
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