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.dohe...@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 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.