missing level in glmer summary output

Question

I have a mind-boggling question regarding the summary output of a glmer model.

In m0.1 below, I'm wondering where the 1st level of Listgp is. It is supposed to be ListgpT.

m0.1 <- glmer(match ~ Listgp + (1|stimulus) + (1|Listener), data = PATdata, family = "binomial")
> summary(m0.1)
Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) [
glmerMod]
 Family: binomial  ( logit )
Formula: match ~ Listgp + (1 | stimulus) + (1 | Listener)
   Data: PATdata

     AIC      BIC   logLik deviance df.resid 
  5218.3   5253.4  -2604.2   5208.3     8203 

Scaled residuals: 
     Min       1Q   Median       3Q      Max 
-21.9276  -0.2804  -0.2059   0.2740   9.4275 

Random effects:
 Groups   Name        Variance Std.Dev.
 Listener (Intercept) 1.676    1.294   
 stimulus (Intercept) 4.949    2.225   
Number of obs: 8208, groups:  Listener, 228; stimulus, 12

Fixed effects:
            Estimate Std. Error z value Pr(>|z|)  
(Intercept)  -1.3754     0.6792  -2.025   0.0429 *
ListgpTA      0.2284     0.3073   0.743   0.4572  
ListgpTQ      0.1432     0.2513   0.570   0.5687  
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
         (Intr) LstgTA
ListgpTA -0.235       
ListgpTQ -0.288  0.636

As can be seen from the output above only ListgpTA and ListgpTQ are shown but not ListgpT.

Could this mean that the results of ListgpT be the same as the Intercept?

Answer 1

That's quite normal in fact. In that case I am guessing that there are only 3 possible cases for Listgp : ListgpT, ListgpTA and ListgpTQ. So there is no need for an output for ListgpT because it is considered as the reference level, meaning that ListgpTA and ListgpTQ are expressed in comparison with ListgpT.

You can read this which presents an output in R and you can see that of the 4 Cancer Stage only 3 are in the output (because it is assumed that the first stage is the default, just as ListgpT is the default in your example)