Re: [R] gam help (really a vegan question)

From: Gavin Simpson <>
Date: Wed, 12 Nov 2008 22:42:51 +0000

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
 ECRC, UCL Geography,          [f] +44 (0)20 7679 0565
 Pearson Building,             [e]
 Gower Street, London          [w]
 UK. WC1E 6BT.                 [w]

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