censboot

Bootstrap for Censored Data

This function applies types of bootstrap resampling which have been suggested to deal with right-censored data. It can also do model-based resampling using a Cox regression model.

Usage

censboot(data, statistic, R, F.surv, G.surv, strata = matrix(1,n,2),
         sim = "ordinary", cox = NULL, index = c(1, 2), …,
         parallel = c("no", "multicore", "snow"),
         ncpus = getOption("boot.ncpus", 1L), cl = NULL)

Details

The various types of resampling are described in Davison and Hinkley (1997) in sections 3.5 and 7.3. The simplest is case resampling which simply resamples with replacement from the observations.

The conditional bootstrap simulates failure times from the estimate of the survival distribution. Then, for each observation its simulated censoring time is equal to the observed censoring time if the observation was censored and generated from the estimated censoring distribution conditional on being greater than the observed failure time if the observation was uncensored. If the largest value is censored then it is given a nominal failure time of Inf and conversely if it is uncensored it is given a nominal censoring time of Inf. This is necessary to allow the largest observation to be in the resamples.

If a Cox regression model is fitted to the data and supplied, then the failure times are generated from the survival distribution using that model. In this case the censoring times can either be simulated from the estimated censoring distribution (sim = "model") or from the conditional censoring distribution as in the previous paragraph (sim = "cond").

The weird bootstrap holds the censored observations as fixed and also the observed failure times. It then generates the number of events at each failure time using a binomial distribution with mean 1 and denominator the number of failures that could have occurred at that time in the original data set. In our implementation we insist that there is a least one simulated event in each stratum for every bootstrap dataset.

When there are strata involved and sim is either "model" or "cond" the situation becomes more difficult. Since the strata for the survival and censoring distributions are not the same it is possible that for some observations both the simulated failure time and the simulated censoring time are infinite. To see this consider an observation in stratum 1F for the survival distribution and stratum 1G for the censoring distribution. Now if the largest value in stratum 1F is censored it is given a nominal failure time of Inf, also if the largest value in stratum 1G is uncensored it is given a nominal censoring time of Inf and so both the simulated failure and censoring times could be infinite. When this happens the simulated value is considered to be a failure at the time of the largest observed failure time in the stratum for the survival distribution.

When parallel = "snow" and cl is not supplied, library(survival) is run in each of the worker processes.

References

Andersen, P.K., Borgan, O., Gill, R.D. and Keiding, N. (1993) Statistical Models Based on Counting Processes. Springer-Verlag.

Burr, D. (1994) A comparison of certain bootstrap confidence intervals in the Cox model. Journal of the American Statistical Association, 89, 1290--1302.

Davison, A.C. and Hinkley, D.V. (1997) Bootstrap Methods and Their Application. Cambridge University Press.

Efron, B. (1981) Censored data and the bootstrap. Journal of the American Statistical Association, 76, 312--319.

Hjort, N.L. (1985) Bootstrapping Cox's regression model. Technical report NSF-241, Dept. of Statistics, Stanford University.

See Also

boot, coxph, survfit

Aliases

• censboot
• cens.return

Examples

# 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)
# }