[R] Time Dependent Cox Model

[quaildoc]

Does anyone have suggestions? Thanks!

quaildoc wrote:
> 
> 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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