[R] [lme4]Coef output with binomial lmer

[Doran, Harold]

The extractor function for the fixed effects is fixef(), not coef(). Out
of curiosity, why are you using (1|ass%in%pop%in%fam)? This notation is
non-standard and does not define the nesting structure of the data.

I think you want (1|ass/pop/fam)

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of Tom Cameron
> Sent: Friday, August 08, 2008 11:47 AM
> To: r-help at r-project.org; r-sig-mixed-models at r-project.org
> Subject: [R] [lme4]Coef output with binomial lmer
> 
> Dear R users  
>  
> I have built the following model
>  
> m1<-lmer(y~harn+foodn+(1|ass%in%pop%in%fam),family = "quasibinomial")
>  
> where y<-cbind(alive,dead)
>  
> where harn and foodn are categorical factors and the random 
> effect is a nested term to represent experimental structure 
> e.g.  Day/Block/Replicate ass= 5 level factor, pop= 2 
> populations per treatment factor in each assay, 7 reps per population
>  
> The model can be family = quasibinomial or binomial
>  
> My complete lack of understanding is in retrieving the 
> coefficients for the fixed effects to back-transform the 
> effects of my factors on proportional survival
>  
> I get the following output:
> > coef(m1)
> $`ass %in% pop %in% fam`
>       (Intercept)      harn1     harn2   foodn2
> FALSE   1.0322375 -0.1939521 0.0310434 0.810084
> TRUE    0.5997679 -0.1939521 0.0310434 0.810084
>  
> Where FALSE and TRUE refer to some attribute of the random effect 
>  
> My hunch is that it refers to the Coefficients with (=TRUE) 
> and without
> (=FALSE) the random effects?
>  
> Any help appreciated
>  
> 
> ..............................................................
> ..........
> ............
> Dr Tom C Cameron
> Genetics, Ecology and Evolution
> IICB, University of Leeds
> Leeds, UK
> Office: +44 (0)113 343 2837
> Lab:    +44 (0)113 343 2854
> Fax:    +44 (0)113 343 2835
> 
> 
> Email: t.c.cameron at leeds.ac.uk
> Webpage: click here
> <http://www.fbs.leeds.ac.uk/staff/profile.php?tag=Cameron_TC> 
> 
>  
> 
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