R/plot.catpredi.survival.R

In CatPredi: Optimal Categorisation of Continuous Variables in Prediction Models

#' Plot the optimal cut points.
#'
#' @param x An object of type catpredi.survival.
#' @param ... Additional arguments to be passed on to other functions. Not yet implemented.
#'
#' @returns
#' This function returns the plot of the relationship between the predictor variable and the outcome.
#'
#' @description Plots the functional form of the predictor variable we want to
#'    categorise. Additionally, the optimal cut points obtained with the
#'    catpredi.survival() function are drawn on the graph.
#'
#' @references I Barrio,  M.X Rodriguez-Alvarez, L Meira-Machado, C Esteban  and
#'    I Arostegui (2017). Comparison of two discrimination indexes in the categorisation
#'     of continuous predictors in time-to-event studies. \emph{SORT}, 41:73-92
#'
#' @author Irantzu Barrio and Maria Xose Rodriguez-Alvarez.
#'
#' @seealso
#' \code{\link{catpredi.survival}}
#'
#' @examples
#' library(CatPredi)
#' library(survival)
#' set.seed(123)
#' #Simulate data
#' n = 500
#' tauc = 1
#' X <- rnorm(n=n, mean=0, sd=2)
#' SurvT <- exp(2*X + rweibull(n = n, shape=1, scale = 1))   + rnorm(n, mean=0, sd=0.25)
#' # Censoring time
#' CensTime <- runif(n=n, min=0, max=tauc)
#' # Status
#' SurvS <- as.numeric(SurvT <= CensTime)
#' # Data frame
#' dat <- data.frame(X = X, SurvT = pmin(SurvT, CensTime), SurvS = SurvS)
#'
#' # Select optimal cut points using the AddFor algorithm
#' res <- catpredi.survival (formula= Surv(SurvT,SurvS)~1, cat.var="X", cat.points = 2,
#'                           data = dat, method = "addfor", conc.index = "cindex", range = NULL,
#'                           correct.index = FALSE)
#' # Plot
#' plot(res)
#'
#' @export
plot.catpredi.survival <-
function(x, ...){
	# Fit the model
	formula <- stats::update(x$formula, stats::as.formula(paste("~ . + pspline(", x$cat.var, ")", sep = "")))
	formula <- stats::as.formula(Reduce(paste, deparse(formula)))
	fit.survival <- survival::coxph(formula, data = x$data)
	pos <- attr(stats::terms.formula(formula, specials = c("pspline")),"specials")$pspline - 1
	stats::termplot(fit.survival, terms = pos, se = TRUE, ylabs = paste0("f(",x$cat.var,")"))
	graphics::abline(v = x$results$cutpoints, lty = 2)
}