[R] Problems with coxph and survfit in a stratified model with interactions

[rm]

Dear Terry, 

Thanks for your valuable comments! Could you please restate the example that
you refer to? If I include cov1 in the data frame, as you suggest, I get the
following error message. Complete code follows.

” Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) : 
  contrasts can be applied only to factors with 2 or more levels"

Regarding Chris’s suggestion, I would prefer not to have the main effect of
cov2 in the model. I would prefer to stick with “~ strata(cov1):cov2” to
keep the interpretation of the regression coefficient straightforward.

Best regards,
Roland



require(survival) 
data(lung) 
# 
lung$cov1 <- as.factor(lung$ph.ecog) 
lung$cov2 <- as.factor(lung$sex) 
levels(lung$cov1)[levels(lung$cov1)==0] <- "zero" 
levels(lung$cov1)[levels(lung$cov1)==1] <- "one" 
levels(lung$cov1)[levels(lung$cov1)==2] <- "two" 
levels(lung$cov1)[levels(lung$cov1)==3] <- "three" 
levels(lung$cov2)[levels(lung$cov2)==1] <- "male" 
levels(lung$cov2)[levels(lung$cov2)==2] <- "female" 
# 
df <- data.frame( 
  cov1=factor("one", levels = levels(lung$cov1)),
  cov2=factor("female", levels = levels(lung$cov2)) 
) 
sCox <- coxph(Surv(time, status) ~ strata(cov1):cov2, data=lung) 
sfCox <- survfit(sCox,newdata=df)



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