R/ordinalizeFunc.R

In MST: Multivariate Survival Trees

ordinalizeFunc <-
function(dat, col.surv, col.id, col.ctg, min.levels = 3, details = FALSE) {
  vnames <- colnames(dat)
  surv <- dat[, col.surv]; id <- dat[, col.id];
  n <- NROW(dat)
  p <- length(col.ctg)
  OUT <- as.list(1:p); names(OUT) <- vnames[col.ctg]
  for (j in 1:p) {
    col <- col.ctg[j]
    vname <- vnames[col]
    x <- as.character(dat[, col])
    x.level <- sort(unique(x))

    # SHOULD WE MERGE SOME LEVELS FIRST?
    tab <- table(x, surv[ , 2])
    if (min(tab) <= min.levels && max(dim(tab)) > 2) print(paste("You might want to merge some levels of", vname, "first before ordinalization."))
    if (details) { print(vname); print(x.level); print(tab) }

    # FITTING MARGINAL MODEL
    fit <- try(suppressWarnings(coxph(surv ~ x + cluster(id), data = dat)), silent = TRUE)
    if (inherits(fit, "try-error")) { betas <- c(baseline = 0, rep(0, length(unique(x)) - 1))
    } else { betas <- c(baseline = 0, coef(fit)) }

    # THE INFORMATION REGARDING "ORDINALIZATION"
    OUT[[j]] <- cbind(x.level, betas, rank = rank(betas))
    if (details) print(OUT[[j]])

    # REPLACE THE COLUMN IN DATA
    x.level.ordered <- x.level[order(betas)]
    x1 <- ordered(x, levels = x.level.ordered)
    dat[, col] <- as.numeric(x1)
  }
  return(list(dat=dat, info=OUT))
}