R help - Jul 2012 - mgcv: Extract random effects from gam model

Hi everyone,

I can't figure out how to extract by-factor random effect adjustments from a
gam model (mgcv package).

Example (from ?gam.vcomp):
library(mgcv)
set.seed(3)
dat <- gamSim(1,n=400,dist="normal",scale=2)
a <- factor(sample(1:10,400,replace=TRUE))
b <- factor(sample(1:7,400,replace=TRUE))
Xa <- model.matrix(~a-1)    ## random main effects
Xb <-  model.matrix(~b-1)
Xab <- model.matrix(~a:b-1) ## random interaction
dat$y <- dat$y + Xa%*%rnorm(10)*.5 + 
  Xb%*%rnorm(7)*.3 + Xab%*%rnorm(70)*.7
dat$a <- a;dat$b <- b

mod <- gam(y ~ s(a, bs="re") + s(x2, k = 15), data = dat)

When I run plot(mod) I can see the adjustments for the "a" factor, but
I
don't know which adjustment is associated with which factor. Is it possible
to extract the information underlying this plot numerically?

Thanks!
Jan



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Hi Jan ,

coef(mod) will extract the coefficients, including for a. They are 
labelled and for 'a' are in the same order as levels(a).

best,
Simon



On 23/07/12 10:08, janvanhove wrote:
> Hi everyone,
>
> I can't figure out how to extract by-factor random effect adjustments
from a
> gam model (mgcv package).
>
> Example (from ?gam.vcomp):
> library(mgcv)
> set.seed(3)
> dat <- gamSim(1,n=400,dist="normal",scale=2)
> a <- factor(sample(1:10,400,replace=TRUE))
> b <- factor(sample(1:7,400,replace=TRUE))
> Xa <- model.matrix(~a-1)    ## random main effects
> Xb <-  model.matrix(~b-1)
> Xab <- model.matrix(~a:b-1) ## random interaction
> dat$y <- dat$y + Xa%*%rnorm(10)*.5 +
>    Xb%*%rnorm(7)*.3 + Xab%*%rnorm(70)*.7
> dat$a <- a;dat$b <- b
>
> mod <- gam(y ~ s(a, bs="re") + s(x2, k = 15), data = dat)
>
> When I run plot(mod) I can see the adjustments for the "a"
factor, but I
> don't know which adjustment is associated with which factor. Is it
possible
> to extract the information underlying this plot numerically?
>
> Thanks!
> Jan
>
>
>
> --
> View this message in context:
http://r.789695.n4.nabble.com/mgcv-Extract-random-effects-from-gam-model-tp4637415.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help at r-project.org mailing list
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> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

-- 
Simon Wood, Mathematical Science, University of Bath BA2 7AY UK
+44 (0)1225 386603               http://people.bath.ac.uk/sw283