[R] GAM, GAMM and numerical integration, help please

Claudia Penaloza claudiapenaloza at gmail.com
Thu May 13 22:59:29 CEST 2010

I am trying to apply methods used by Chaloupka & Limpus (1997) (
http://www.int-res.com/articles/meps/146/m146p001.pdf) to my own turtle
growth data.

I am having trouble with two things...

1) After the GAM is fit, the residuals are skewed.

>m1 <- gam(growth~s(mean.size,

>plot(m1, scale=0) #figure attached

Should I try fitting a GAMM to model the tendencies in the residuals?

2) Using the GAM, I am able to fit a cubic-b spline but I do not know how to
determine the equation for this spline nor how to integrate it/differentiate
it (to obtain plots similar to 3c & f in Chaloupka & Limpus (1997)).
What should I do next?

>size <- seq(100,600,along.with=fitted(m1))

>grw <- fitted(m1)

>bspline3 <- gam(grw~s(size, bs="cr", k=3))

>plot(grw~size,ylab="Growth (mm/yr)", xlab="Curved Carapace Length
(mm)")         #figure attached

>lines(fitted(bspline3)~size, lwd=2)

Thank you very much for any help!

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