survtab: age standardisation

[kseppa]

In survtab(..., surv.method="lifetable") age-standardised estimate should be calculated, although an age-specific survival estimate would be 0. An example: age-standardised 5-year survival is missing, if patients in the oldest age group died within the first 1 year after diagnosis:

data("sire", package = "popEpi")
library(Epi)
library(survival)
library(data.table)

#include patients over 70 years of age who died within the first 1 year
sire <- sire[dg_age<70 | (dg_age>=70 & (ex_date-dg_date)<365 & status==1)]

x <- Lexis(entry = list(FUT = 0, AGE = dg_age, CAL = get.yrs(dg_date)), 
           exit = list(CAL = get.yrs(ex_date)), 
           data = sire[sire$dg_date < sire$ex_date, ],
           exit.status = factor(status, levels = 0:2, 
                                labels = c("alive", "canD", "othD")), 
           merge = TRUE)

data("popmort", package = "popEpi")
pm <- data.frame(popmort)
names(pm) <- c("sex", "CAL", "AGE", "haz")
## ICSS weights usage
data("ICSS", package = "popEpi")
cut <- c(0, 30, 50, 70, Inf)
agegr <- cut(ICSS$age, cut, right = FALSE)
w <- aggregate(ICSS1~agegr, data = ICSS, FUN = sum)
x$agegr <- cut(x$dg_age, cut, right = FALSE)

st <- survtab(FUT ~ 1, data = x, subset=dg_age>=70,
              surv.type = "surv.rel",
              pophaz = pm, weights = w$ICSS1,surv.method = "lifetable",
              breaks = list(FUT = seq(0, 5, 1/12)))
summary(st,t=5) ##survival=0 in 70+ age group

st <- survtab(FUT ~ adjust(agegr), data = x, 
              surv.type = "surv.rel",
              pophaz = pm, weights = w$ICSS1,surv.method = "lifetable",
              breaks = list(FUT = seq(0, 5, 1/12)))
summary(st,t=5) ##This should be calculated, too.