Dear friends,
I met some problem on using GAM() function in R.
Any help or suggestions are greatly appreciated.
# My programs and problems are list below#
library(splines)
library(gam)
point<-read.csv("d:/gam.csv",sep=",",header=TRUE) #read
the data
gam.opt<-gam(mark~lo(x,y,span=0.2)+lo(lstday2004,span=0.2)+lo(slope,span=0.2)+lo(ndvi2004,span0.2)+lo(elevation,span=0.2)+disbinary,
family=binomial(logit),data=point) #span
is 0.2
#when you run the above codes, 30 warnings() appear
> warnings()
Warning message$B!'(B
1: In lo.wam(x, z, wz, fit$smooth, which, fit$smooth.frame, ... :
lo.wam convergence not obtained in 30 iterations
2: In lo.wam(x, z, wz, fit$smooth, which, fit$smooth.frame, ... :
lo.wam convergence not obtained in 30 iterations
.............................................
gam.opt2<-gam(mark~lo(x,y,span=0.05)+lo(lstday2004,span=0.05)+lo(slope,span0.05)+lo(ndvi2004,span=0.05)+lo(elevation,span=0.05
)+disbinary,family=binomial(logit),data=point) #span is 0.05
#22 warnings()
> warnings()
1: In lo.wam(x, z, wz, fit$smooth, which, fit$smooth.frame, ... :
k-d tree limited by memory; nvmax= 226
2: In lo.wam(x, z, wz, fit$smooth, which, fit$smooth.frame, ... :
pseudoinverse used at 14923
3: In lo.wam(x, z, wz, fit$smooth, which, fit$smooth.frame, ... :
neighborhood radius 1
4: In lo.wam(x, z, wz, fit$smooth, which, fit$smooth.frame, ... :
reciprocal condition number 0
........................................................
Q1: Their warning messages were differernt, are there any problem with the
codes that i used? What does these warnings mean?
Q2: As we know, the span is an important role for smoothing, so i try to
choose the optimal span by the AIC criterion. But it seemed that i can't run
it successfully,
My codes are listed below.
hmin<-0.05; hmax<-0.95; hstart<-hmin; nh<-100
hstep<-(hmax-hmin)/(nh-1)
aic.h<- matrix(NA,nrow=nh,ncol=2)
for (i in 1:nh)
{
htry<-hstart+(i-1)*hstep m.gam
<-gam(mark~lo(x,y,span=htry)+lo(lstday2004,span=htry)+lo(slope,span=htry)+lo(ndvi2004,span=htry)+lo(elevation,span=htry)+disbinary,family=binomial(logit),data=point)
aic.h[i,2]<-m.gam$aic
aic.h[i,1]<-htry
}
aic.h #only the first line in aic.h has values, there must be errors in my
codes
Where goes wrong? How should i do for determining the best span for
different variables?
Any help or suggestions are greatly appreciated?
BTW, I'd like to send you my dataset off this mailing list if possible.
--
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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