R/FUN-CSRplot.R

In VZoche-Golob/AFTtools: Tools for the Data Preparation, Fitting and Diagnostics of Accelerated Failure Times Models

#' Cox-Snell-Residual Plot
#'
#' Plots the Cox-Snell-Residuals of a model fitted using \code{\link[survival]{survreg}}
#'  against the Kaplan-Meier estimator of their cumulative hazard.
#'
#' @note If the \code{model} includes frailties, they have to be estimated with
#'  \code{sparse = FALSE} to allow the residuals to be extracted.
#'
#' @param model An object of class \code{\link[survival]{survreg}}.
#'
#' @references
#'  P. Glomb, „Statistische Modelle und Methoden in der Analyse von Lebenszeitdaten“,
#'  Diplomarbeit, Carl-von-Ossietzky-Universität, Oldenburg, 2007.
#' @references
#'  C. P. Farrington, ‘Residuals for Proportional Hazards Models with Interval-Censored
#'  Survival Data’, Biometrics, vol. 56, no. 2, pp. 473–482, 2000.
#'
#' @import survival
#' @importFrom magrittr '%>%'
#'
#' @export
CSRplot <- function(model) {

  assertive::assert_is_all_of(model, "survreg")



  res <- -log(predict(model)) %>%
   {survfit(Surv(., model$y[, ncol(model$y)] > 0) ~ 1)}



  plot(res$time, -log(res$surv), type = "b",
       lty = 1, pch = 20, col = "red",
       xlab = "Cox-Snell-Residuals", ylab = "Cumulative hazard")
  abline(0, 1, lty = 2)

}