R/cindex.R

In csetraynor/survbayes2: Bayesian Survival Models (survbayes2)

#' Get c-index
#'
#'
#' The efficacy of the survival model can be measured by
#'  the concordance statistic
#'
#' @param data For the default functions, a datframe containing survival
#' (time), and status (0:censored/1:event), and the explanatory variables.
#' @param mod Coxph model object fitted with coxph (survival).
#' @return A cindex object
#' @seealso [coxph]
#' @keywords cindex
#' @examples
#' require(survival)
#' require(dplyr)
#' data(lung)
#' lung <- lung %>%
#' mutate(status = (status == 2))
#'
#' mod <- coxph(Surv(time, status)~ age, data = lung)
#'
#' get_cindex(lung, mod)
#'
#' @export get_cindex
#' @author Carlos S Traynor
#' @references
#'
#'  Terry M. Therneau and Patricia M. Grambsch (2000).
#'   _Modeling Survival Data: Extending the Cox Model_.
#'   Springer, New York. ISBN 0-387-98784-3.
#'   @export get_cindex
#'
get_cindex <- function(data, mod,...)
  UseMethod("get_cindex")

#' @export
#' @rdname get_cindex
get_cindex <-
  function(x, mod, ...) {
    
    train_data <- rsample::analysis(x)
    
    timepoints <-  seq(0, max(train_data$time),
                       length.out = 100L)
    
    test_data <- rsample::assessment(x)
    
    
    tail(suppressWarnings(suppressMessages( (pec::cindex(mod, 
                                        Surv(time, status) ~ 1,
                                        data = test_data,
                                    pred.times = timepoints,
               eval.times = timepoints))))$AppCindex$coxph , n=1)
  }