Dear Simon,
Sorry for an incomplete listing of the question.
#mgcv version is  1.3-29, R 2.6.1, windows XP
#m.gam<-gam(mark~s(x)+s(y)+s(lstday2004)+s(ndvi2004)+s(slope)+s(elevation)+disbinary,family=binomial(logit),data=point)
The above program's the core codes in my following loop programs.
 It works well if i run the above codes only one time for my dataset, but
warnings will occur if i run many times for the following loop.

> while (j<1001) {
+  index=sample(ID, replace=F)
+  m.data$x=coords[index,]$x
+  m.data$y=coords[index,]$y
+  # For each permutation, we run the GAM using the optimal span for the
above model m.gam
+  s.gam
<-gam(mark~s(x)+s(y)+s(lstday2004)+s(ndvi2004)+s(slope)+s(elevation)+disbinary,,sp=c(
5.582647e-07,4.016504e-02,2.300424e-04,1.274065e+03,9.558236e-09,
1.868827e-08),family=binomial(logit),data=m.data)
+  permresults[,i]=predict.gam(s.gam)
+  i=i+1
+  if (j%%100==0) print(i)
+  j=j+1
+  }
[1] 101
[1] 201
[1] 301
[1] 401
[1] 501
[1] 601
[1] 701
[1] 801
[1] 901
[1] 1001
warnings() over 50
> warnings()
1: In gam.fit(G, family = G$family, control = control, gamma = gamma,  ... :
  fitted probabilities numerically 0 or 1 occurred
......................................
14: In gam.fit(G, family = G$family, control = control, gamma = gamma,  ...
:
  Algorithm did not converge
..........................

On Dec 17, 2007 4:54 PM, Simon Wood <s.wood@bath.ac.uk> wrote:

> What mgcv version are you running (and on what platform)?
>
> n Thursday 13 December 2007 17:46, zhijie zhang wrote:
> > Dear all,
> >  I run the GAMs (generalized additive models) in gam(mgcv) using the
> > following codes.
> >
> > m.gam
> >
> <-gam(mark~s(x)+s(y)+s(lstday2004)+s(ndvi2004)+s(slope)+s(elevation)+disbin
> >ary,family=binomial(logit),data=point)
> >
> >  And two repeated warnings appeared.
> > Warnings$B!'(B
> > 1: In gam.fit(G, family = G$family, control = control, gamma = gamma,
>  ...
> > : Algorithm did not converge
> >
> > 2: In gam.fit(G, family = G$family, control = control, gamma = gamma,
>  ...
> > : fitted probabilities numerically 0 or 1 occurred
> >
> > Q1: For warning1, could it be solved by changing the value of
> > mgcv.toloptions for
> > gam.control(mgcv.tol=1e-7)?
> >
> > Q1: For warning2, is there any impact for the results if the "fitted
> > probabilities numerically 0 or 1 occurred" ?  How can i solve it?
> >
> >  I didn't try the possible solutions for them, because it took such a
> > longer time to run the whole programs.
> >  Could anybody suggest their solutions?
> >  Any help or suggestions are greatly appreciated.
> >   Thanks.
>
> --
> > Simon Wood, Mathematical Sciences, University of Bath, Bath, BA2 7AY UK
> > +44 1225 386603  www.maths.bath.ac.uk/~sw283
>



-- 
With Kind Regards,

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Zhi Jie,Zhang ,PHD
Tel:+86-21-54237149
Dept. of Epidemiology,School of Public Health,Fudan University
Address:No. 138 Yi Xue Yuan Road,Shanghai,China
Postcode:200032
Email:epistat@gmail.com
Website: www.statABC.com
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