[R] How to choose a proper smoothing spline in GAM of mgcv package?

David Winsemius dwinsemius at comcast.net
Tue Oct 13 04:46:18 CEST 2009

On Oct 12, 2009, at 10:10 PM, Yan Li wrote:

> Hi, there,
> I have 5 datasets. I would like to choose a basis spline with same  
> knots in
> GAM function in order to obtain same basis function for 5 datasets.
> Moreover, the basis spline is used to for an interaction of two  
> covarites.

It is possible to specify the knots for cr splines in the gam function  
(... not GAM). You have not described the sampling process that  
resulted in these 5 datasets, but the naive approach would be to cbind  
them and estimate for the super-group as a whole. After finding knots  
for a pooled dataset you could perhaps refit individually with the  
knots being fixed at the group values, assuming this makes sense for  
you sampling design.
> I used "cr" in one covariate, but it can only smooth w.r.t 1  
> covariate. Can
> anyone give me some suggestion about how to choose a proper  
> smoothing spline
> (bs='?') and knots for two covariates?

Multiple terms in the model require vectors for the argument to sp or  
else inclusion within each smoothing term. See the docs and examples in:


Have you yet looked at:



David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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