glmer with/without intercept gave different results

-----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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