[R-sig-ME] Boosting computation time of glmmPQL when specifying spatial, correlation structure

[Highstat Statistics Ltd]

On 17/01/2010 11:00, r-sig-mixed-models-request at r-project.org wrote:
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> I know how to speed up GAMM when specifying a spatial correlation structure by splitting up the dataset to compute the

You are not splitting up the data set. Instead you are imposing the 
correlation on a sub-block of data.

> spatial correlation coefficients of corSpher.
> such (if dataG is my dataset)
> cutx<-cut(dataG$x,breaks=(4))                          cuty<- cut(dataG$y, breaks=(4))
> cutxy<- paste(cutx, cuty)
>
> and then
> gamm(Response~(var1)+s(var2),family=binomial, data=dataG,correlation=corSpher(form=~(x+y)|cutxy)).
>
> the cutxy doesn't seem to work with glmmPQL and with 1500 points, it takes ages...
> Does anyone know if there is a way to apply the same "trick" ?
>    

The first thing to do is to use decent starting values for the range 
(and nugget???). See
?corSpher

Alain


> By the way (take a breath...), does the plotting of a spatial correlogram with residuals(model, type="pearson") from a glmmPQL model (where correlation structure was specified) makes sense to you ? I'm not sure if residuals of such model account for the stucture (and I can hear some of you, why don't you check this by yourself... yes , I will try !)
>
> Best regards and thanks for any hint
>
> Alex
>
> Alexandre Villers
> PhD. Candidate
> Team Agripop
> CEBC CNRS UPR 1934
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-- 


Dr. Alain F. Zuur
First author of:

1. Analysing Ecological Data (2007).
Zuur, AF, Ieno, EN and Smith, GM. Springer. 680 p.
URL: www.springer.com/0-387-45967-7


2. Mixed effects models and extensions in ecology with R. (2009).
Zuur, AF, Ieno, EN, Walker, N, Saveliev, AA, and Smith, GM. Springer.
http://www.springer.com/life+sci/ecology/book/978-0-387-87457-9


3. A Beginner's Guide to R (2009).
Zuur, AF, Ieno, EN, Meesters, EHWG. Springer
http://www.springer.com/statistics/computational/book/978-0-387-93836-3


Other books: http://www.highstat.com/books.htm


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