inst/calc.LL.quantile.ex.R

In cuRe: Parametric Cure Model Estimation

##Use data cleaned version of the colon cancer data from the rstpm2 package
data("colonDC")
set.seed(2)
colonDC <- colonDC[sample(1:nrow(colonDC), 1000), ]

##Extract general population hazards
colonDC$bhaz <- general.haz(time = "FU", rmap = list(age = "agedays", sex = "sex", year= "dx"),
                            data = colonDC, ratetable = survexp.dk)

#Fit cure model and estimate cure point
fit <- rstpm2::stpm2(Surv(FUyear, status) ~ 1, data = colonDC, df = 6,
                     bhazard = colonDC$bhaz, cure = TRUE)
calc.LL.quantile(fit, q = 1,
                 rmap = list(age = agedays, sex = sex, year = dx))