R/vim.Surv.R

In logicFS: Identification of SNP Interactions

vim.Surv <- function (mprimes, mat.eval, inbagg, cl, score)
{
  if (score != "PL"){
    uni.death.times <- sort(unique(cl[, 1][cl[, 2] == 1]))
    n.death <- length(uni.death.times)
  }
  primes <- unique(unlist(mprimes))
  n.trees <- length(mprimes)
  n.primes <- length(primes)
  id.primes <- colnames(mat.eval) %in% primes
  oob <- which(!(1:nrow(mat.eval)) %in% inbagg)
  vec.improve <- numeric(ncol(mat.eval))
  names(vec.improve) <- colnames(mat.eval)
  if ((n.primes == 1) & (score == "PL")){
    vec.improve[id.primes] <- vimCox.oneprime(mat.eval[, id.primes], 
                                              cl, oob, inbagg)
    return(vec.improve)
  }
  mat.in <- cbind(1 - diag(n.primes), 1)
  rownames(mat.in) <- primes
  list.eval <- lapply(mprimes, function (x, e = mat.eval, i = mat.in) 
    e[, x, drop = FALSE] %*% i[x, , drop = FALSE] > 0)
  le.vec <- n.primes + 1
  vec.ll <- numeric(le.vec)
  getIth <- function (x, ids = NULL) x[, ids]
  for (i in 1:le.vec){
    mat.model <- matrix(unlist(lapply(list.eval, getIth, 
                                      ids = i)), ncol = n.trees)
    if (score == "PL"){
      vec.ll[i] <- getCoxScore(cl, mat.model, inbagg, oob)
    } else {vec.ll[i] <- getSurvivalScore(mat.model, inbagg, oob, cl, score, 
                                          uni.death.times, n.death)
    }
  }
  vec.ll <- vec.ll - vec.ll[le.vec]
  vec.improve[primes] <- vec.ll[-le.vec]
  if (score == "PL"){
    vec.improve <- -2 * vec.improve
  } else if (score != "Brier"){
    vec.improve <- -1 * vec.improve
  }
  vec.improve
}