R/coxtab.R

In shenhanjie/statsTBL: Create Analysis Table Results

#' Cox Regression Table Results
#'
#' Generate Hazard Ratio Table
#' @param data Input data (data.frame)
#' @param survfma A formula object of coxph function,
#' @param option Type of table structure (option = "1" or option  = "2")
#' @return Table Results of Hazard Ratio with P-values
#' @details Hazard Ratio is calculated by Cox Regression.
#' @examples
#' @export
#' coxtab function



coxtab <- function(data,survfma,option){

  cox.mod <- coxph(survfma,data)
  sum.cox <- summary(cox.mod)

  if (option == "1"){
    tab <- matrix(NA,dim(sum.cox$coefficients)[1],2)
    colnames(tab) <- c("HR (95% CI)","P-value")
    rownames(tab) <- rownames(sum.cox$coefficients)
    for (i in 1:dim(sum.cox$coefficients)[1]){
      tab[i,1] <- paste0(format(sum.cox$coefficients[i,2],nsmall=2,digits=2),"  (",
                         format(sum.cox$conf.int[i,3],nsmall=2,digits=2),", ",
                         format(sum.cox$conf.int[i,4],nsmall=2,digits=2),")")
      tab[i,2] <- format(sum.cox$coefficients[i,5],nsmall=2,digits=2)
    }
  }

  if (option == "2"){
    tab <- matrix(NA,dim(sum.cox$coefficients)[1],3)
    colnames(tab) <- c("HR","95% CI" ,"P-value")
    rownames(tab) <- rownames(sum.cox$coefficients)
    for (i in 1:dim(sum.cox$coefficients)[1]){
      tab[i,1] <- format(sum.cox$coefficients[i,2],nsmall=2,digits=2)
      tab[i,2] <- paste0("(",format(sum.cox$conf.int[i,3],nsmall=2,digits=2),", ",
                         format(sum.cox$conf.int[i,4],nsmall=2,digits=2),")")
      tab[i,3] <- format(sum.cox$coefficients[i,5],nsmall=2,digits=2)
    }
  }

  return(tab)

}