R/getBrier.R

In logicFS: Identification of SNP Interactions

getBrier <- function (mat.oob.eche, cl, uni.death.times)
{
  if (nrow(mat.oob.eche) != nrow(cl)){
    stop("nrow(mat.oob.eche) != nrow(cl)")
  }
  
  n.death <- length(uni.death.times)
  time <- cl[, 1]
  ot <- order(time)
  cens <- cl[ot, 2]
  time <- time[ot]
  cl <- Surv(time, cens)
  mat.oob.eche <- mat.oob.eche[ot, ]
  cl.cens <- cl
  cl.cens[, 2] <- !cl[, 2]
  survs <- mat.oob.eche
  
  hatcdist <- survfit(cl.cens ~ 1)
  csurv <- getCsurv(hatcdist, cl)
  csurv[csurv == 0] <- Inf
  
  csurv.death <- getCsurvDeath(csurv, cl, uni.death.times)
  
  bsc <- rep(0, n.death)
  
  for (j in 1:n.death){
    help1 <- as.integer(time <= uni.death.times[j] & cens == 1)
    help2 <- as.integer(time > uni.death.times[j])
    bsc[j] <- mean((0 - survs[, j])^2 * help1 * (1/csurv) + 
                     (1 - survs[, j])^2 * help2 * (1/csurv.death[j]))
  }
  idx <- 2:n.death
  RET <- diff(uni.death.times) %*% ((bsc[idx - 1] + bsc[idx])/2)
  RET <- RET/diff(range(time))
  
  return(RET)
}