[R-sig-ME] R-sig-mixed-models Digest, Vol 72, Issue 1

[chico3 at sapo.pt]

I Ben,


I think that you are right. Thank you so much for your answer. I was  
almost given up :).


Cheers,


Francisco




[snip]

> I have four luminaires randomly distributed. Two luminaires have  
> light  on and two luminaires have no light. Below the luminaires I  
> have two  treatments. Each treatment has four replicates that were  
> randomly  distributed below the luminaires. Moreover, I have made  
> all the  possible combinations of presence absence of light and  
> treatments.
>
> I want to check if there is a effect of each treatment and the   
> interactions between all the combinations.The response variable is a  
>  proportion (number of specific specie/total number of species)
>
> Treatment1<-as.factor(“Yes”,”No”)
> Treatment2<- as.factor(“Yes”,”No”)
> Light<- as.factor(“Yes”,”No”)
> Response<-cbind(number_of_specific_species, total_species)
>
> I have made this model,
>
>   model<-glmer(Response ~ Treatment1*Treatment2 + (1|Light), family=binomial)
>
> However this doesn´t allow to see the effect of light or the   
> interaction between light and treatments. Moreover, I don´t know how  
>  to include overdispersion, since glmer doesn´t allow quasi families  
>  such as glm.
>
> I know this is a simple question, but I greatly would appreciate  
> some  clues on how to proceed.

I may be missing something here, but it doesn't make sense to me
to treat Light as a random effect (one criterion -- the levels "Light"
and "No light" aren't *exchangeable*, i.e. you couldn't switch
the factor labels without changing the meaning of the experiment).
I would say you are looking for something more like

glmer(Response ~ Treatment1*Treatment2*Light + (1|luminaire), family=binomial)

where the luminaires are labeled uniquely (e.g.
"Light1","Light2","Nolight1","Nolight2")

It sounds like this is a randomized block design (i.e. every level of
Treat1*Treat2 is present at each luminaire), so you could test the
interaction between Treat1*Treat2 and luminaire via
(Treat1*Treat2|luminaire) instead of (1|luminaire) (see e.g.
Schielzeth 2009), although you may find that this leads to estimates
of zero variance (overfitting the data).