R help - Mar 2008 - unexpected GAM result - at least for me!

Hi


I am afraid i am not understanding something  very fundamental.... and does not
matter how much i am looking into the book "Generalized Additive
Models"  of S. Wood i still don't understand my result.

I am trying to model presence / absence (presence = 1, absence = 0) of a species
using some lidar metrics (i have 4 of these). I am using different models and
such .... and when i used gam i got this very weird (for me) result which i
thought it is not possible - or i have no idea how to interpret it.
> can3.gam <- gam(can>0~s(be)+s(crr)+s(ch)+s(home), family =
'binomial')
> summary(can3.gam)
Family: binomial
Link function: logit
Formula:
can> 0 ~ s(be) + s(crr) + s(ch) + s(home)
Parametric coefficients:
            Estimate Std. Error z value Pr(>|z|)
(Intercept)    85.39     162.88   0.524      0.6
Approximate significance of smooth terms:
          edf Est.rank Chi.sq p-value
s(be)   1.000        1  0.100   0.751
s(crr)  3.929        8  0.380   1.000
s(ch)   6.820        9  0.396   1.000
s(home) 1.000        1  0.314   0.575
R-sq.(adj) =      1   Deviance explained =  100%
UBRE score = -0.81413  Scale est. = 1         n = 148

Is this a perfect fit with no statistical significance, an over-estimating or
what???? It seems that the significance of the smooths terms is
"null". Of course with such a model i predict perfectly presence /
absence of species.

Again, i hope you don't mind i'm asking you this. Any explanation will
be very much appreciated.

Thanks,

Monica

PS. I've contacted the author of the book who is the package maintainer as
well but until now i didn't get a reply.

_________________________________________________________________


esh_realtime_042008

On 3/31/2008 8:34 AM, Monica Pisica wrote:
> 
> Hi
> 
> 
> I am afraid i am not understanding something  very fundamental.... and does
not matter how much i am looking into the book "Generalized Additive
Models"  of S. Wood i still don't understand my result.
> 
> I am trying to model presence / absence (presence = 1, absence = 0) of a
species using some lidar metrics (i have 4 of these). I am using different
models and such .... and when i used gam i got this very weird (for me) result
which i thought it is not possible - or i have no idea how to interpret it.
> 
>> can3.gam <- gam(can>0~s(be)+s(crr)+s(ch)+s(home), family =
'binomial')
>> summary(can3.gam)
> Family: binomial
> Link function: logit
> Formula:
> can> 0 ~ s(be) + s(crr) + s(ch) + s(home)
> Parametric coefficients:
>             Estimate Std. Error z value Pr(>|z|)
> (Intercept)    85.39     162.88   0.524      0.6
> Approximate significance of smooth terms:
>           edf Est.rank Chi.sq p-value
> s(be)   1.000        1  0.100   0.751
> s(crr)  3.929        8  0.380   1.000
> s(ch)   6.820        9  0.396   1.000
> s(home) 1.000        1  0.314   0.575
> R-sq.(adj) =      1   Deviance explained =  100%
> UBRE score = -0.81413  Scale est. = 1         n = 148
> 
> Is this a perfect fit with no statistical significance, an over-estimating
or what???? It seems that the significance of the smooths terms is
"null". Of course with such a model i predict perfectly presence /
absence of species.
> 
> Again, i hope you don't mind i'm asking you this. Any explanation
will be very much appreciated.
Look at the data.  You can get a perfect fit to a logistic regression 
model fairly easily, and it looks as though you've got one.  (In fact, 
the huge intercept suggests that all predictions will be 1.  Do you 
actually have any variation in the data?)

Duncan Murdoch