why do I not have an intercept in glmer model (fixed effects)?

[grietjie]

Hi all!
I'm testing what effects chick feldging success (FledgeAD). Chicks who fledged successfully is '1' and those who died is '0'. Therefore I used glmer with binominal family. My fixed effect are mean temperature (meanT), individual number of chick (IndNum) and species (3 species). Random effect is season (3 breeding seasons).

For some reason the intercept for the fixed effects are not showing. Anyone know why and how I can get the intercept? The summary() output does not show the intercept of fixed effects

This is what I've tried thus far.

library(lme4)
fledge.mod1 <-glmer(FledgeAD ~ 0 + meanT + IndNum + Species + (1|Season), family = binomial, data = season.nofem1)
summary(fledge.mod1)

Generalized linear mixed model fit by maximum likelihood (Laplace Approximation) [glmerMod]
Family: binomial ( logit )
Formula: FledgeAD ~ 0 + meanT + IndNum + Species + (1 | Season)
Data: season.nofem1

 AIC      BIC   logLik deviance df.resid 

100.7 117.5 -44.4 88.7 115

Scaled residuals:
Min 1Q Median 3Q Max
-3.8364 -0.2846 0.1684 0.3747 11.1878

Random effects:
Groups Name Variance Std.Dev.
Season (Intercept) 0.5984 0.7735
Number of obs: 121, groups: Season, 3

Fixed effects:
Estimate Std. Error z value Pr(>|z|)
meanT -0.6264 0.1806 -3.469 0.000523 ***
IndNum -1.7247 0.3495 -4.935 8.01e-07 ***
SpeciesAGH 30.1561 6.9351 4.348 1.37e-05 ***
SpeciesRBH 29.6886 6.6451 4.468 7.90e-06 ***
SpeciesYBH 30.1913 6.9766 4.328 1.51e-05 ***

Signif. codes: 0 ‘’ 0.001 ‘’ 0.01 ‘’ 0.05 ‘.’ 0.1 ‘ ’ 1

Correlation of Fixed Effects:
meanT IndNum SpcAGH SpcRBH
IndNum 0.226
SpeciesAGH -0.971 -0.425
SpeciesRBH -0.968 -0.446 0.994
SpeciesYBH -0.973 -0.425 0.994 0.995

[FJCC]

I have not used lme4, but doesn't having 0 at the beginning of the formula remove the intercept. The formula help says "A model with no intercept can be also specified as y ~ x + 0 or y ~ 0 + x."

[grietjie]

Thank you! You have saved me a lot of time!