ODSDesignIC {ICODS} | R Documentation |
Outcome-Dependent Sampling with Interval-Censored Failure Time Data
Description
Provides an outcome-dependent sampling (ODS) design with interval-censored failure time data, where the observed sample is enriched by selectively including certain more informative failure subjects. The method is a sieve semiparametric maximum empirical likelihood approach for fitting the proportional hazards model to data from the interval- censoring ODS design.
Usage
ODSDesignIC(U, V, del1, del2, z, mVal, ind, a1, a2, beta = NULL,
maxit = 10L, verbose = TRUE, ...)
Arguments
U |
numeric vector (n); examination time. See Details for further information. |
V |
numeric vector (n); examination time. See Details for further information. |
del1 |
integer vector (n); indicator of a left-censored observation I(T<=U). See Details for further information. |
del2 |
integer vector (n); indicator of an interval-censored observation I(U<T<=V). See Details for further information. |
z |
matrix (nxp); covariates. |
mVal |
integer vector (m); one or more options for the degree of the Bernstein polynomials. If more than one option provided, the value resulting in the lowest AIC is selected. The results returned are for only that m-value. |
ind |
integer vector (n); indicating membership of the simple random sample (0), lower-tail supplemental sample (1), or upper-tail supplemental sample (2). |
a1 |
numeric (1); lower cut-off point for selecting ODS sample (0 < a1 < a2 < tau). |
a2 |
numeric (1); upper cut-off point for selecting ODS sample (0 < a1 < a2 < tau). |
beta |
numeric vector (p); initial values for beta. If NULL, initial guess set to 0.5 for each of the p parameters. |
maxit |
integer(1); maximum number of calls to optimization method. |
verbose |
logical; TRUE generates progress screen prints. |
... |
optional inputs to "control" of function optim(). |
Details
The implementation uses stats::optim() to minimize the likelihood. The hard-coded method is "BFGS". Users are able to make changes to the 'control' input of optim() by passing named inputs through the ellipses. If a call to optim() returns convergence = 1, i.e., optim() reached its internal maximum number of iterations before convergence was attained, the software automatically repeats the call to optim() with input variable par set to the last parameter values. This procedure is repeated at most maxit times.
Input parameters U, V, del1, and del2 are defined as follows. Suppose there are K follow-up examinations at times TE = (T1, T2, ..., TK), and the failure time is denoted as TF. For left-censored data, the failure occurred prior to the first follow-up examination (TF < T1); therefore, define U = T1, V = tau, and (del1,del2)=(1,0). For right-censored data, the failure had not yet occurred at the last follow-up examination (TF > TK); therefore, define U = 0, V = TK, and (del1,del2)=(0,0). For interval-censored data, the failure occurred between two follow-up examinations, e.g. T2 < TF < T3; therefore, define U and V to be the two consecutive follow-up examination times bracketing the failure time TF and (del1,del2)=(0,1).
Value
an object of class ODSDesign (inheriting from ICODS) containing
optim |
a list of the results returned by optim(). |
beta |
the estimated beta parameters. |
se |
the standard error of the estimated beta parameters. |
pValue |
the p-value of the estimated beta parameters. |
m |
the selected degree of the Bernstein polynomials. |
AIC |
the AIC value for the selected degree of the Bernstein polynomials. |
References
Zhou, Q., Cai, J., and Zhou, H. (2018). Outcome-dependent sampling with interval-censored failure time data. Biometrics, 74(1): 58–67. <doi:10.1111/biom.12744>
Examples
data(odsData)
result <- ODSDesignIC(U = odsData$U,
V = odsData$V,
del1 = odsData$del1,
del2 = odsData$del2,
z = odsData$z,
mVal = 1L,
ind = odsData$ind,
a1 = 0.43,
a2 = 0.45,
beta = NULL,
maxit = 10L,
verbose = TRUE)
print(result)
mVal(result)
estimate(result)
optimObj(result)
minAIC(result)
summary(result)