[R] Time Dependent Cox Model

[joris meys]

Well,

it might be wise to elaborate a bit more about the variables and what
exactly you want e.g. death-time to be. I'd interprete it as time of
death, but the fact that it is 0/1, means it is a logical (?) binary
variable of some sort.

Please ask your question in such a way that somebody who doesn't know
the dataset and your research, can still understand what is inside the
dataset and what exactly you're trying to obtain.

I'd also suggest to add the command to read in the data. I don't have
the time to spend looking around how exactly I can read in the dataset
in such a way it fits what you have in your workspace.

Cheers
Joris

On Wed, Oct 14, 2009 at 5:37 PM, quaildoc <just.struttin at gmail.com> wrote:
>
> 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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