R/aftgee_pkg.R

In aftgee: Accelerated Failure Time Model with Generalized Estimating Equations

#' aftgee: Accelerated Failure Time with Generalized Estimating Equation
#'
#' A package that uses Generalized Estimating Equations (GEE) to estimate
#' Multivariate Accelerated Failure Time Model (AFT).
#' This package implements recently developed inference procedures for
#' AFT models with both the rank-based approach and the least squares approach.
#' For the rank-based approach, the package allows various weight choices
#' and uses an induced smoothing procedure that leads to much more
#' efficient computation than the linear programming method.
#' With the rank-based estimator as an initial value, the generalized
#' estimating equation approach is used as an extension of the least
#' squares approach to the multivariate case.
#' Additional sampling weights are incorporated to handle missing data
#' needed as in case-cohort studies or general sampling schemes.
#'
#' @aliases aftgee-packages
#' @references Chiou, S., Kim, J. and Yan, J. (2014) Marginal Semiparametric Multivariate
#' Accelerated Failure Time Model with Generalized Estimating Equation.
#' \emph{Life Time Data}, \bold{20}(4): 599--618.
#' @references Chiou, S., Kang, S. and Yan, J. (2014) Fast Accelerated Failure Time Modeling
#' for Case-Cohort Data. \emph{Statistics and Computing}, \bold{24}(4): 559--568.
#' @references Chiou, S., Kang, S. and Yan, J. (2014) Fitting Accelerated Failure Time Model
#' in Routine Survival Analysis with {R} Package \pkg{aftgee}.
#' \emph{Journal of Statistical Software}, \bold{61}(11): 1--23.
#' @references Huang, Y. (2002) Calibration Regression of Censored Lifetime Medical Cost.
#' \emph{Journal of American Statistical Association}, \bold{97}, 318--327.
#' @references Jin, Z. and Lin, D. Y. and Ying, Z. (2006)
#' On Least-squares Regression with Censored Data. \emph{Biometrika}, \bold{90}, 341--353.
#' @references Johnson, L. M. and Strawderman, R. L. (2009)
#' Induced Smoothing for the Semiparametric Accelerated Failure Time Model:
#' Asymptotic and Extensions to Clustered Data. \emph{Biometrika}, \bold{96}, 577 -- 590.
#' @references Zeng, D. and Lin, D. Y. (2008)
#' Efficient Resampling Methods for Nonsmooth Estimating Functions.
#' \emph{Biostatistics}, \bold{9}, 355--363
#'
#' @importFrom MASS ginv
#' @importFrom BB BBsolve dfsane
#' @importFrom survival Surv survfit basehaz coxph
#' @importFrom geepack geese geese.fit
#' @importFrom parallel makeCluster clusterExport stopCluster detectCores parSapply parLapply
#' @importFrom methods getClass
#' @importFrom graphics boxplot
#' @importFrom stats approx coef complete.cases lm model.extract model.matrix pnorm printCoefmat
#' @importFrom stats rexp rnorm var vcov weights as.formula
#' @importFrom utils vi
#' @importFrom Rcpp sourceCpp
#'
#' @useDynLib aftgee, .registration = TRUE
#' @docType package
"_PACKAGE"
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