[R] Cox model -missing data.

[(Ted Harding)]

Hi Aoife,
I think that if you simply replace each "*" in the data file
with "NA", then it should work ("NA" is usually interpreted
as "missing" for those functions for which missingness is
relevant). How you subsequently deal with records which have
missing values is another question (or many questions ... ).

So your data should look like:

V1       V2          V3               Survival       Event
ann      13          WTHomo           4                1
ben      20          NA               5                1
tom      40          Variant          6                1

Hoping this helps,
Ted.

On 19-Dec-2014 10:12:00 aoife doherty wrote:
> Hi all,
> 
> I have a data set like this:
> 
> Test.cox file:
> 
> V1        V2         V3               Survival       Event
> ann      13          WTHomo           4                1
> ben      20          *                5                1
> tom      40          Variant          6                1
> 
> 
> where "*" indicates that I don't know what the value is for V3 for Ben.
> 
> I've set up a Cox model to run like this:
> 
>#!/usr/bin/Rscript
> library(bdsmatrix)
> library(kinship2)
> library(survival)
> library(coxme)
> death.dat <- read.table("Test.cox",header=T)
> deathdat.kmat <-2*with(death.dat,makekinship(famid,ID,faid,moid))
> sink("Test.cox.R.Output")
> Model <- coxme(Surv(Survival,Event)~ strata(factor(V1)) +
> strata(factor(V2)) + factor(V3)) +
> (1|ID),data=death.dat,varlist=deathdat.kmat)
> Model
> sink()
> 
> 
> 
> As you can see from the Test.cox file, I have a missing value "*". How and
> where do I tell the R script "treat * as a missing variable". If I can't
> incorporate missing values into the model, I assume the alternative is to
> remove all of the rows with missing data, which will greatly reduce my data
> set, as most rows have at least one missing variable.
> 
> Thanks
> 
>       [[alternative HTML version deleted]]
> 
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-------------------------------------------------
E-Mail: (Ted Harding) <Ted.Harding at wlandres.net>
Date: 19-Dec-2014  Time: 10:21:23
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