R/tablecompet.R

In akashpawarstat/progcomprisk: Performs Cox PH on survival and competing events. Returns list and data set for DEGs contributing for survival and competing events (progcomprisk)

#' tablecompet
#'
#' 'tablecompet' function from 'progcomprisk' package enables user to input a
#' data and calculate the proportions of types of status in column 'Status'.
#'
#' @export
#' @param data Data frame consisting survival events such, 'Id', 'OS', 'PFS', 'Death', 'Prog'.
#' @examples
#' tablecompet(user_data)
#'
#' @details
#' 'tablecompet(data) adds a new column 'Status' to the input
#' dataset and assigns status 0, 1, 2 to each cell. It assigns 0 when progression is
#' 1, death is 0 or progression 0 death is 0, assigns 1 when progression is 1 and
#' death is 1, whereas assigns 2 when progression is 0 and death is 1.
#'
#' Concern should be given to rename the columns of the input data before using 'progcomprisk' package, as follows.
#'
#' 1) Subject Id column should be named as 'Id'.
#'
#' 2) OS column must be named as 'OS' .
#'
#' 3) Death status/event column should be named as 'Death'.
#'
#' 4) PFS column should be named as 'PFS'.
#'
#' 5) Progression event column should be named as 'Prog'.
#'
tablecompet <- function(data){

  data$Status[data$Prog == 0 & data$Death == 1] <- 2
  data$Status[data$Prog == 0 & data$Death == 0] <- 0
  data$Status[data$Prog == 1 & data$Death == 1] <- 1
  data$Status[data$Prog == 1 & data$Death == 0] <- 0

  print(data)
  print("Column 'Status' added to the input data")
  table(data$Status)
}