[R] gam help (really a vegan question)

Gavin Simpson gavin.simpson at ucl.ac.uk
Wed Nov 12 23:42:51 CET 2008

On Tue, 2008-11-11 at 23:56 -0500, stephen sefick wrote:
> What does Generalized Cross Validation score mean.  I preform and
> ordisurf on an ordination (nmds) with an environmental variable.  I am
> trying to figure out "how well" the environmental varibles
> predict/explain the sites placements in species space.  Any help would
> be greatly appreciated.  Any pointers to literature... would be
> welcome.
> thanks in advance,

GCV is used to select the degree of smoothing in the smooth functions of
a linear predictor of a GAM model fitted via package mgcv. The GCV score
is the statistic that is at it's minimum when the "optimal" level of
smoothing is achieved. You can compare models fitted by mgcv::gam on the
basis of their GCV scores.

But this is nothing to do with vegan; vegan just uses mgcv::gam to do
the surface fitting. Check out the help for mgcv and/or take a look at
Simon Wood's excellent book on GAMs (and a whole lot more) Generalized
Additive Models: An Introduction with R:



 Dr. Gavin Simpson             [t] +44 (0)20 7679 0522
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