# NOT RUN {
library(survival)
# Example 3.9 of Davison and Hinkley (1997) does a bootstrap on some
# remission times for patients with a type of leukaemia. The patients
# were divided into those who received maintenance chemotherapy and
# those who did not. Here we are interested in the median remission
# time for the two groups.
data(aml, package = "boot") # not the version in survival.
aml.fun <- function(data) {
surv <- survfit(Surv(time, cens) ~ group, data = data)
out <- NULL
st <- 1
for (s in 1:length(surv$strata)) {
inds <- st:(st + surv$strata[s]-1)
md <- min(surv$time[inds[1-surv$surv[inds] >= 0.5]])
st <- st + surv$strata[s]
out <- c(out, md)
}
out
}
aml.case <- censboot(aml, aml.fun, R = 499, strata = aml$group)
# Now we will look at the same statistic using the conditional
# bootstrap and the weird bootstrap. For the conditional bootstrap
# the survival distribution is stratified but the censoring
# distribution is not.
aml.s1 <- survfit(Surv(time, cens) ~ group, data = aml)
aml.s2 <- survfit(Surv(time-0.001*cens, 1-cens) ~ 1, data = aml)
aml.cond <- censboot(aml, aml.fun, R = 499, strata = aml$group,
F.surv = aml.s1, G.surv = aml.s2, sim = "cond")
# For the weird bootstrap we must redefine our function slightly since
# the data will not contain the group number.
aml.fun1 <- function(data, str) {
surv <- survfit(Surv(data[, 1], data[, 2]) ~ str)
out <- NULL
st <- 1
for (s in 1:length(surv$strata)) {
inds <- st:(st + surv$strata[s] - 1)
md <- min(surv$time[inds[1-surv$surv[inds] >= 0.5]])
st <- st + surv$strata[s]
out <- c(out, md)
}
out
}
aml.wei <- censboot(cbind(aml$time, aml$cens), aml.fun1, R = 499,
strata = aml$group, F.surv = aml.s1, sim = "weird")
# Now for an example where a cox regression model has been fitted
# the data we will look at the melanoma data of Example 7.6 from
# Davison and Hinkley (1997). The fitted model assumes that there
# is a different survival distribution for the ulcerated and
# non-ulcerated groups but that the thickness of the tumour has a
# common effect. We will also assume that the censoring distribution
# is different in different age groups. The statistic of interest
# is the linear predictor. This is returned as the values at a
# number of equally spaced points in the range of interest.
data(melanoma, package = "boot")
library(splines)# for ns
mel.cox <- coxph(Surv(time, status == 1) ~ ns(thickness, df=4) + strata(ulcer),
data = melanoma)
mel.surv <- survfit(mel.cox)
agec <- cut(melanoma$age, c(0, 39, 49, 59, 69, 100))
mel.cens <- survfit(Surv(time - 0.001*(status == 1), status != 1) ~
strata(agec), data = melanoma)
mel.fun <- function(d) {
t1 <- ns(d$thickness, df=4)
cox <- coxph(Surv(d$time, d$status == 1) ~ t1+strata(d$ulcer))
ind <- !duplicated(d$thickness)
u <- d$thickness[!ind]
eta <- cox$linear.predictors[!ind]
sp <- smooth.spline(u, eta, df=20)
th <- seq(from = 0.25, to = 10, by = 0.25)
predict(sp, th)$y
}
mel.str <- cbind(melanoma$ulcer, agec)
# this is slow!
mel.mod <- censboot(melanoma, mel.fun, R = 499, F.surv = mel.surv,
G.surv = mel.cens, cox = mel.cox, strata = mel.str, sim = "model")
# To plot the original predictor and a 95% pointwise envelope for it
mel.env <- envelope(mel.mod)$point
th <- seq(0.25, 10, by = 0.25)
plot(th, mel.env[1, ], ylim = c(-2, 2),
xlab = "thickness (mm)", ylab = "linear predictor", type = "n")
lines(th, mel.mod$t0, lty = 1)
matlines(th, t(mel.env), lty = 2)
# }
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