np_elife: Nonparametric estimation of the survival function

In longevity: Statistical Methods for the Analysis of Excess Lifetimes

Nonparametric estimation of the survival function

Description

The survival function is obtained through the EM algorithm described in Turnbull (1976); censoring and truncation are assumed to be non-informative. The survival function changes only at the J distinct exceedances y_i-u and truncation points.

Usage

np_elife(
  time,
  time2 = NULL,
  event = NULL,
  type = c("right", "left", "interval", "interval2"),
  thresh = 0,
  ltrunc = NULL,
  rtrunc = NULL,
  tol = 1e-12,
  weights = NULL,
  method = c("em", "sqp"),
  arguments = NULL,
  ...
)

Arguments

time	excess time of the event of follow-up time, depending on the value of event
time2	ending excess time of the interval for interval censored data only.
event	status indicator, normally 0=alive, 1=dead. Other choices are TRUE/FALSE (TRUE for death). For interval censored data, the status indicator is 0=right censored, 1=event at time, 2=left censored, 3=interval censored. Although unusual, the event indicator can be omitted, in which case all subjects are assumed to have experienced an event.
type	character string specifying the type of censoring. Possible values are "right", "left", "interval", "interval2".
thresh	double thresh
ltrunc	lower truncation limit, default to NULL
rtrunc	upper truncation limit, default to NULL
tol	double, relative tolerance for convergence of the EM algorithm
weights	double, vector of weights for the observations
method	string, one of "em" for expectation-maximization (EM) algorithm or "sqp" for sequential quadratic programming with augmented Lagrange multiplie method.
arguments	a named list specifying default arguments of the function that are common to all elife calls
...	additional arguments, currently ignored

Details

The unknown parameters of the model are p_j (j=1, \ldots, J) subject to the constraint that \sum_{j=1}^J p_j=1.

Value

a list with elements

• cdf: right-continuous stepfun object defined by probabilities

• time: matrix of unique values for the Turnbull intervals defining equivalence classes; only those with non-zero probabilities are returned

• prob: J vector of non-zero probabilities

• niter: number of iterations

References

Turnbull, B. W. (1976). The Empirical Distribution Function with Arbitrarily Grouped, Censored and Truncated Data. Journal of the Royal Statistical Society. Series B (Methodological) 38(3), 290–295.

Gentleman, R. and C. J. Geyer (1994). Maximum likelihood for interval censored data: Consistency and computation, Biometrika, 81(3), 618–623.

Frydman, H. (1994). A Note on Nonparametric Estimation of the Distribution Function from Interval-Censored and Truncated Observations, Journal of the Royal Statistical Society. Series B (Methodological) 56(1), 71-74.

Examples

set.seed(2021)
n <- 20L
# Create fake data
ltrunc <- pmax(0, runif(n, -0.5, 1))
rtrunc <- runif(n, 6, 10)
dat <- samp_elife(n = n,
                  scale = 1,
                  shape = -0.1,
                  lower = ltrunc,
                  upper = rtrunc,
                  family = "gp",
                  type2 = "ltrt")
npi <- np_elife(time = dat,
                rtrunc = rtrunc,
                ltrunc = ltrunc)
print(npi)
summary(npi)
plot(npi)

longevity documentation built on Nov. 12, 2023, 5:07 p.m.