R/GenDat_KJ.r

In OneArm2stage: Phase II Single-Arm Two-Stage Designs with Time-to-Event Outcomes

##' Generate survival data with restricted follow-up Using Weibull Distribution.
##'
##' @title Generate Survival Data with unrestricted Follow-Up
##' @param shape shape parameter for WB distributions.
##' @param S_fixed survival probability at the fixed time point x_fixed.
##' @param x_fixed a fixed time point where the survival probability is known.
##' @param rate a constant accrual rate.
##' @param tf the follow-up time.
##' @param t1 the interim analysis time.
##' @param n sample size.
##' @param seed seed used for the random sample generation.
##' @return Two dataframes: data (the full data for final analysis) and data_t1 (the data for interim analysis), both containing the following 4 variables:\cr
##'             \emph{Entry} time when each patient enters the trial, assumed to be uniform from 0 to ta with ta as the time when enrollment ends.\cr
##'             \emph{time} the time under observation during entire trial (in data) or before t1 (in data_t1) for each patient.\cr
##'             \emph{status} the status indicator of patients (event = 1, censored = 0), which can be different between data and data_t1.\cr
##'             \emph{Total} the sum of \emph{Entry} and \emph{time}.
##' @import stats
##' @keywords internal
GenDat_KJ <- function(shape, S_fixed, x_fixed, rate, tf, t1, n, seed) {
  set.seed(seed)
  ta = n/rate
  MTSL = ta + tf

  # dist = "WB"
    scale0 = x_fixed/(-log(S_fixed))^(1/shape)
    time = rweibull(n, shape, scale = scale0)

  # unordered
  A = runif(n, 0, ta)

  Cens = as.numeric(time < MTSL - A)
  # time is the true failure time

  Time = pmax(0,pmin(time, MTSL - A))
  # the observed time capped by MTSL-A

  #### generate Full data #######
  data=data.frame(Entry=A, time=Time, status=Cens, Total=A+Time) # Total = entry+observed time

  ### generate stage I data ######
  data_t1=data[(data$Entry<=t1),]
  ind_cens=which(data_t1$Total>t1)
  data_t1$status<-replace(data_t1$status, ind_cens, 0)
  data_t1$time<-replace(data_t1$time, ind_cens, t1-data_t1$Entry[ind_cens])


  return(list(data=data, data_t1=data_t1))
}