[R-sig-ME] contrast in glmer

[Douglas Bates]

At the end of your query you mention that you didn't know of a place
to send such queries other than to the package authors.  The best
place to send such queries is the to R-SIG-Mixed-Models at R-project.org
mailing list, which I am cc:ing on this reply.

On Mon, Dec 19, 2011 at 10:14 AM, Magalì Matteodo
<magali.matteodo at gmail.com> wrote:
> Dear Mr Bates,
> I'm a master student in the Lausanne University and I'm doing the data
> analysis for my master thesis. I'm using the function glmer from package
> lme4 in R. It's from some days that I'm trying to understand the contrast
> option in the function but I don't come to a conclusion.
>
>
> I'm working on a list of alpine plants found in different summits at
> different altitudes; I would like to understand if the plant summit
> colonization ability can be explained by the trait "Pollen_vector" and if
> there is an interaction between the altitude and the biological trait.
> The response variable is Colonization_event and it's a binary variable.
>
>> names(my.data)
> [1] "Species_name"       "Colonization_event" "Summit_name"
> "Summit_altitude"    "Pollen_vector"
>
>> attach(my.data)
>
>> levels(Pollen_vector)
> [1] "F"  "in" "j"  "se" "wi"
>
>> library(lme4)
>
>> require(vegan)
>> Summit_altitude_z= decostand(Summit_altitude, "standardize")
>
>> model_Int0<-glmer(Colonization_event~(Summit_altitude_z*Pollen_vector)
> +(1|Summit_name)+(1|Species_name),data=my.data,family=binomial(link=logit),na.action=na.exclude)
>> summary(model_Int0)
>
> Which is the contrast method used by default in glmer? Is that the treatment
> contrast?

Like most model-fitting methods in R that rely on a linear predictor,
glmer outsources construction of the model matrix to the function
model.matrix so the question really comes down to how model.matrix
behaves.  It uses the default contrasts specified in the "contrasts"
option.  The factory-fresh setting is

> getOption("contrasts")
        unordered           ordered
"contr.treatment"      "contr.poly"

If you want to change this for all factors you can reset that option.
If you want to change it for only one factor then you can set the
contrasts attribute on that particular factor (see ?contrasts for more
explanation) or specify the name of the contrasts-generating function
in a named lists given as the contrasts argument passed to glmer (see
?model.matrix for more details).  It might also help to run

example(contrasts)

and

example(model.matrix)

> I would like to use the Sum contrast, how I can specify it to R?
> I tried to construct the model in this way:
>
>>model_Int0_s<-glmer(Colonization_event~(Summit_altitude_z*Pollen_vector)
> +(1|Summit_name)+(1|Species_name),data=my.data,family=binomial(link=logit),na.action=na.exclude,contrast=contr.sum)
> summary(model_Int0_s)
>
> and in this one:
>>options(contrast=contr.sum)
>>model_Int0<-glmer(Colonization_event~(Summit_altitude_z*Pollen_vector)
> +(1|Summit_name)+(1|Species_name),data=my.data,family=binomial(link=logit),na.action=na.exclude,contrast=T)
> summary(model_Int0)
>
> and the same repeated with contrast=contr.treatment and
> contrast=contr.helmert, but the estimate values in the summary are always
> the same. Why? How to fit the model with a particular contrast?
>
> I perfectly understand that is not the common practice to ask such things
> right to the author but I didn't know what to do differently. I hope that
> you can help me to come out of this stinker.
>
> Thanks,
>
> best regards,
>
> Magalì Matteodo