R/breast.R

In success: Survival Control Charts Estimation Software

#' @title Survival after breast cancer surgery
#'
#' @description Data about patient survival after their breast cancer surgery procedure
#' performed at one of the 15 units participating in a cancer treatment study.
#' The data is based on a trial performed at the European Organisation for
#' Research and Treatment of Cancer (EORTC).
#'
#' @format A \code{data.frame} with 2663 rows and 11 variables:
#' \describe{
#'   \item{entrytime}{Chronological time of entry of patient into study/time of surgery (numeric)}
#'   \item{survtime}{Time from entry until failure of patient (numeric)}
#'   \item{censorid}{Censoring indicator (0 - right censored, 1 - observed) (integer)}
#'   \item{unit}{Unit number at which patient received treatment (integer)}
#'   \item{var1-7}{Covariates associated with patient (factor)}
#' }
#'
#'
#' @source Based on trial data from the European Organisation for Research and
#' Treatment of Cancer, \url{https://www.eortc.org/}
#'
#' @examples
#' #Determine the estimated arrival rate for all units in the data
#' arrival_rate(breast)
#'
#' #Plot Quality Control charts for unit 11 in the study
#' library(survival)
#' phmodbreast <- coxph(Surv(survtime, censorid) ~ . - entrytime - unit ,
#' data = breast)
#' glmmodbreast <- glm((survtime <= 36) & (censorid == 1) ~ . - entrytime - unit,
#'  data = breast, family = binomial(link = "logit"))
#'
#' par(mfrow = c(1, 3))
#' p1 <- plot(cgr_cusum(data = subset(breast, unit == 11),  coxphmod = phmodbreast)) +
#' ggtitle("CGR-CUSUM")
#' p2 <- plot(bk_cusum(data = subset(breast, unit == 11),  coxphmod = phmodbreast,
#'  theta = log(2))) + ggtitle("BK-CUSUM")
#' p3 <- plot(bernoulli_cusum(data = subset(breast, unit == 11), followup = 36,
#'  glmmod = glmmodbreast, theta = log(2))) + ggtitle("Bernoulli CUSUM")
#' p4 <- plot(funnel_plot(data = breast, glmmod = glmmodbreast, followup = 36 )) +
#' ggtitle("Funnel plot")
#'
#' if(require("gridExtra")){
#'  grid.arrange(p1, p2, p3, p4, nrow = 2)
#' }
#'
"breast"