[R] case weights in coxph (survival)

[Nicholas Lewin-Koh]

Hi,
I am having trouble with the survival library, particualrily the coxph
function.

the following works
coxph(jtree9$cph.call,z,rep(1,dim(z)[1]))
Call:
coxph(formula = jtree9$cph.call, data = z, weights = rep(1, dim(z)[1]))


                   coef exp(coef) se(coef)      z       p
SM               0.2574     1.294   0.0786  3.274 1.1e-03
Sex             -0.1283     0.880   0.1809 -0.709 4.8e-01
RACE            -0.3226     0.724   0.0817 -3.950 7.8e-05
MHHT:MHDM        0.0524     1.054   0.0574  0.913 3.6e-01
FHHT:FHCAD:FHDM  0.0361     1.037   0.0412  0.877 3.8e-01

Likelihood ratio test=43.8  on 5 df, p=2.55e-08  n= 646 

but 
> coxph(jtree9$cph.call,z,rep(1,dim(z)[1]))$weights
NULL

while the documentation says that a coxph object should have a weights
element if supplied. Further (what I am really trying to do) if I put this
in a function

optimize.W<-function(W,G,Groups,cph.call,z){
  n<-length(Groups)
  grp.wt<-rep(0,n)
  for(i in 1:length(G)){
    ind<-Groups == G[i]
    grp.wt[ind]<-W[i]
  }
  mod<-coxph(cph.call,z,grp.wt,na.action=na.omit,singular.ok=T)
  sum(mod$residuals^2)
}

> optimize.W(rep(1,13),unique(jtree9$members[,jtree9$depth]),jtree9$members[,jtree9$depth],
jtree9$cph.call,z)

Error in eval(expr, envir, enclos) : Object "grp.wt" not found

I'm puzzled, is this some sort of environment problem?
 Here's my R particulars

> R.Version()
$platform
[1] "i686-pc-linux-gnu"
$arch
[1] "i686"
$os
[1] "linux-gnu"
$system
[1] "i686, linux-gnu"
$status
[1] ""
$major
[1] "1"
$minor
[1] "3.1"
$year
[1] "2001"
$month
[1] "08"
$day
[1] "31"
$language
[1] "R"

I am also using the most recent version of survival from cran.

Thanks
Nicholas



                 CH3
                  |
                  N             Nicholas Lewin-Koh
                 / \            Dept of Statistics
           N----C   C==O        Program in Ecology and Evolutionary Biology
          ||   ||   |           Iowa State University
          ||   ||   |           Ames, IA 50011
          CH    C   N--CH3      http://www.public.iastate.edu/~nlewin
            \  / \ /            nlewin at iastate.edu
             N    C
             |   ||             Currently
            CH3   O             Graphics Lab
                                School of Computing
                                National University of Singapore
     The Real Part of Coffee    kohnicho at comp.nus.edu.sg

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