[R] GAMM : how to use a smoother for some levels of a variable, and a linear effect for other levels?

Simon Wood s.wood at bath.ac.uk
Fri Apr 16 16:42:30 CEST 2010

Both versions of this should have worked, but you are right that the first 
version didn't when used with `gamm', I've fixed this for mgcv 1.6-2 
(`mgcv:gam' was ok). Thanks for this.


On Wednesday 14 April 2010 09:03, JANSEN, Ivy wrote:
> Hi,
> I was reading the book on "Mixed Effects Models and Extensions in
> Ecology with R" by Zuur et al.
> In Section 6.2, an example is discussed where a gamm-model is fitted,
> with a smoother for time, which differs for each value of ID (4
> different bird species). In earlier versions of R, the following code
> was used
> BM2<-gamm(Birds~Rain+ID+
>        s(Time,by=as.numeric(ID=="Stilt.Oahu"))+
>        s(Time,by=as.numeric(ID=="Stilt.Maui"))+
>        s(Time,by=as.numeric(ID=="Coot.Oahu"))+
>        s(Time,by=as.numeric(ID=="Coot.Maui")),
>      correlation=corAR1(form=~Time |ID ),
>      weights=varIdent(form=~1|ID))
> However, in the current version of R, this does not work anymore, and
> should be changed into
> BM2<-gamm(Birds~Rain+ID+
>        s(Time,by=ID),
>      correlation=corAR1(form=~Time |ID ),
>      weights=varIdent(form=~1|ID))
> It turns out that 2 of the 4 smoothers have estimated degrees of freedom
> of 1, so a linear effect would be sufficient.
> Now my question is how I need to change the code in order to have a time
> smoother for ID=Coot.Oahu and ID=Coot.Maui, and a linear time effect for
> ID=Stilt.Oahu and ID=Stilt.Maui. With the "old" R-code, this seems
> trivial, but I don't have any idea how to do it in the newest R-version
> (interactions with a dummy variable do not work in gamm).
> Thanks,
> Ivy
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> Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> +44 1225 386603  www.maths.bath.ac.uk/~sw283

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