[R] Cox model -missing data.

[aoife doherty]

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

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