[R] Time Dependent Cox Model

[quaildoc]

I am having trouble formatting some survival data to use in a time dependent
cox model. My time dep. variable is habitat and I have it recorded for every
day (with some NAs).  I think it is working properly except for calculating
the death.time. This column should be 1s or 0s and as I have it only
produces 0s.  Any help will be greatly appreciated.


http://www.nabble.com/file/p25881478/Survival_master2.csv
Survival_master2.csv 



 Here is my code:
sum(!is.na(surv[,16:726]))

surv2<-matrix(0,12329,19)
colnames(surv2)<-c('start', 'stop', 'death.time',
names(surv)[1:15],'habitat')
row<-0 # set record counter to 0
    for (i in 1:nrow(surv)) { # loop over individuals
        for (j in 16:726) { # loop over 726 days
          if (is.na(surv[i, j])) next # skip missing data
          else {
            row <- row + 1 # increment row counter
            start <- j - 11 # start time (previous day)
            stop <- start + 1 # stop time (day)
            death.time <- if (stop == surv[i, 4] && surv[i, 5] ==1) 1 else 0
                   # construct record:
            surv2[row,] <- c(start, stop, death.time, unlist(surv[i, c(1:15,
j)]))
            }
        }
   }
surv2<-as.data.frame(surv2)
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