R/HAL9001.R

In riskRegression: Risk Regression Models and Prediction Scores for Survival Analysis with Competing Risks

#' @title Fitting HAL for use with predictRisk
#'
#' @description Fit HAL models via a formula and a data set for use with \code{\link{predictRisk}}.
#' @name Hal9001
#'
#' @param formula A formula.
#' @param data The data on which to fit the model. 
#' @param lambda The tuning parameters for HAL. If set to NULL, then it the parameters are chosen for you.
#' @param \dots Additional arguments that are passed on to the hal_fit.
#' @export
Hal9001 <- function(formula,data,lambda=NULL,...){
  requireNamespace("hal9001")
  strata.num = start = status = NULL
  EHF = prodlim::EventHistory.frame(formula,data,unspecialsDesign = TRUE,specials = NULL)
  stopifnot(attr(EHF$event.history,"model")[[1]] == "survival")
  # blank Cox object needed for predictions
  data = data.frame(cbind(EHF$event.history,EHF$design))
  bl_cph <- coxph(Surv(time,status)~1,data=data,x=1,y=1)
  bl_obj <- coxModelFrame(bl_cph)[]
  bl_obj[,strata.num:=0]
  data.table::setorder(bl_obj, strata.num,stop,start,-status)
  hal_fit <- do.call(hal9001::fit_hal,list(X = EHF$design,
                                           Y = EHF$event.history,
                                           family = "cox",
                                           return_lasso = TRUE,
                                           yolo = FALSE,
                                           lambda = lambda,
                                           ...))
  out = list(fit = hal_fit,
             surv_info = bl_obj,
             call = match.call(),
             terms = terms(formula))
  class(out) = "Hal9001"
  out
}