[R] Cox model -missing data.

[Shouro Dasgupta]

First recode the *  in NA: death.dat$v3[death.dat$v1==*] <- NA

Include this in your model: na.rm=TRUE

Or you could create a new dataset: newdata <- na.omit(death.dat)

Shouro




On Fri, Dec 19, 2014 at 11:12 AM, aoife doherty <aoife.m.doherty at gmail.com>
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
>
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>
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