summary.survtab {popEpi} | R Documentation |
Summarize a survtab Object
Description
Summary method function for survtab
objects; see
survtab_ag
. Returns estimates at given time points
or all time points if t
and q
are both NULL
.
Usage
## S3 method for class 'survtab'
summary(object, t = NULL, subset = NULL, q = NULL, ...)
Arguments
object |
a |
t |
a vector of times at which time points (actually intervals that
contain t) to print summary table of survival function estimates by strata;
values not existing in any interval cause rows containing only |
subset |
a logical condition to subset results table by
before printing; use this to limit to a certain stratum. E.g.
|
q |
a named |
... |
unused; required for congruence with other |
Details
Note that this function returns the intervals and NOT the time points corresponding to quantiles / estimates corresponding to time points. If you want precise estimates at time points that are not interval breaks, add the time points as breaks and re-estimate the survival time function. In interval-based estimation, the estimates denote e.g. probability of dying during the interval, so time points within the intervals are not usually considered at all. See e.g. Seppa, Dyba, and Hakulinen (2015).
Value
A 'data.table': a slice from 'object' based on 't', 'subset', and 'q'.
Author(s)
Joonas Miettinen
References
Seppa K., Dyba T. and Hakulinen T.: Cancer Survival, Reference Module in Biomedical Sciences. Elsevier. 08-Jan-2015. doi:10.1016/B978-0-12-801238-3.02745-8
See Also
Other survtab functions:
Surv()
,
lines.survtab()
,
plot.survtab()
,
print.survtab()
,
survtab()
,
survtab_ag()
Examples
library(Epi)
## NOTE: recommended to use factor status variable
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)
## pretend some are male
set.seed(1L)
x$sex <- rbinom(nrow(x), 1, 0.5)
## observed survival
st <- survtab(Surv(time = FUT, event = lex.Xst) ~ sex, data = x,
surv.type = "cif.obs",
breaks = list(FUT = seq(0, 5, 1/12)))
## estimates at full years of follow-up
summary(st, t = 1:5)
## interval estimate closest to 75th percentile, i.e.
## first interval where surv.obs < 0.75 at end
## (just switch 0.75 to 0.5 for median survival, etc.)
summary(st, q = list(surv.obs = 0.75))
## multiple quantiles
summary(st, q = list(surv.obs = c(0.75, 0.90), CIF_canD = 0.20))
## if you want all estimates in a new data.frame, you can also simply do
x <- as.data.frame(st)