curelps.extract: Extract estimates of survival functions and cure probability...

In blapsr: Bayesian Inference with Laplace Approximations and P-Splines

Extract estimates of survival functions and cure probability for the promotion time cure model.

Description

The routine takes as input an object of class curelps and computes estimates of the baseline survival curve, the population survival curve and the cure probability on a specified time vector. Approximate pointwise credible intervals are available.

Usage

curelps.extract(object, time = NULL, curvetype = c("baseline", "population", "probacure"),
                covar.profile, compute.cred = TRUE, cred.int = 0.95, verbose = TRUE)

Arguments

object	An object of class curelps.
time	A vector of time values on which to compute the estimates. Each component of time must be between 0 and the largest observed follow-up time.
curvetype	The curve on which estimates are computed ; baseline (the default) is for the baseline survival, population is for the population survival function for a profile of covariates given in covar.profile, and probacure is for the probability to be cured (for a profile of covariates given in covar.profile) given that the subject has survived until time t.
covar.profile	A numeric vector of the same length as the number of covariates in the model. This corresponds to the profile of covariates for which to compute the population survival function and cure probability estimates. The order of the covariates in covar.profile is the same as the order specified in formula of the curelps routine. Each component of covar.profile should be in the range of the observed values for the corresponding covariate. If covar.profile is left unspecified by the user, the default will be to take the median covariate values.
compute.cred	Should credible intervals be computed? Default is TRUE.
cred.int	The level for an approximate pointwise credible interval. Default is 0.95.
verbose	Should estimates be printed to console?

Value

A list with the following components:

fit.time	Estimates on the time values provided in time.
cred.int	The chosen level to construct approximate pointwise credible intervals.
covar.profile	The chosen profile of covariates.

Author(s)

Oswaldo Gressani [e-mail].

See Also

curelps, curelps.object, plot.curelps, print.curelps.

Examples

# Example on phase III clinical trial e1684 on melanoma data

data(ecog1684)

# Kaplan-Meier curve
plot(survfit(Surv(time, status) ~ 1, data = ecog1684), mark.time = TRUE)
fit <- curelps(Surv(time, status) ~ lt(age + trt+ sex) +
             st(age + trt + sex), data = ecog1684, K = 20, penorder = 2)
fit
profile1 <- c(0, 1, 1, 0, 1, 1) # Mean age, trt = IFN, sex = Female.
profile2 <- c(0, 0, 1, 0, 0, 1) # Mean age, trt = control, sex = Female.

# Extract cure probabilities
curelps.extract(fit, time = c(0, 1, 2, 3), curvetype = "probacure",
                covar.profile = profile1, cred.int = 0.90)
curelps.extract(fit, time = c(0, 1, 2, 3), curvetype = "probacure",
                covar.profile = profile2, cred.int = 0.90)

blapsr documentation built on Aug. 20, 2022, 5:05 p.m.