Problems with coxph and survfit in a stratified model with interactions
Your df object (newdata) has to have ALL the variables in it. Normally you wouldn't need the strata variable, but in this case cov1 is also a covariate. Look at the example I gave earlier. Terry T.
On 10/15/2012 05:00 AM, r-help-request at r-project.org wrote:
Many thanks for your very quick reply! I tried replacing ?~ strata(cov1) +
cov1:cov2 ? with ?~ strata(cov1):cov2 ?. As a result, I get an error
message saying that ?object 'cov1' not found?. I guess R refers to the data
frame. Any idea how to fix the error? Complete code follows.
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(
cov2=factor("female", levels = levels(lung$cov2))
)
sCox<- coxph(Surv(time, status) ~ strata(cov1):cov2, data=lung)
sfCox<- survfit(sCox,newdata=df)