This question is about what happens to the Hazard Ratio reference level in a Cox PH regression using factors, when the default reference level gets subsetted out, and specifically if that behaviour can be changed within the coxph subset operation.
The application is Cause Specific Hazards, so I'd like the flexibility to analyse multiple subsets of the variables - one for each of the competing risks - without creating multiple instances of the All Cause data set. (Note: this is exploratory, not testing a hypothesis.)
Define a contrived df that behaves reasonably (e.g. statistically significant, not too many warnings)...
smpls = 50
df <- data.frame(time=c(sample.int(10,smpls, replace=TRUE),
sample.int(20,smpls, replace=TRUE),
sample.int(30,smpls, replace=TRUE)),
status=1,
x=as.factor(c(rep("A",smpls),
rep("B",smpls),
rep("C",smpls))))
Load the relevant library...
require(survival)
Do a base case which outputs HR coefficients for B and C, with factor A as the reference...
coxph(Surv(time, status) ~ x, df)
Then subset out factor A. This seems to have the effect of selecting factor C as the reference for the coefficient for factor B.
coxph(Surv(time, status) ~ x, df, subset=x!="A")
In that last example, how would I 'force' the reference to be B instead of C?