R/summary.R

In katehu/addhazard: Fit Additive Hazards Models for Survival Analysis

#' @importFrom stats printCoefmat pnorm

#' @export
summary.ah <- function(object, ...) {
  options(digits = 5)
  ci.lower <- object$coef - 1.96 * object$se
  ci.upper <- object$coef + 1.96 * object$se
  z <- object$coef/object$se
  p.value <- 2 * pnorm(-abs(z))
  TAB <- cbind(coef = object$coef, se = object$se, lower.95 = ci.lower, upper.95 = ci.upper, 
               z = z, p.value = p.value)
  if (dim(TAB)[1] == 1) {
    rownames(TAB) = as.character(object$formula[[3]])  # retrieve the covariate name
  } else {
    rownames(TAB) = names(object$coef)
  }
  res <- list(call = object$call, coefficients = TAB)
  class(res) <- "summary.ah"
  res
}

#' @export
print.summary.ah <- function(x, digits = max(getOption("digits") - 4, 4), signif.stars = getOption("show.signif.stars"), 
                             ...) {
  cat("Call:\n")
  print(x$call)
  cat("\n")
  printCoefmat(x$coefficients, digits = digits, signif.stars = signif.stars, P.values = TRUE, 
               has.Pvalue = TRUE, ...)
}

#' @export
summary.ah.ph2.only <- function(object, ...) {
  options(digits = 5)
  ci.lower <- object$coef - 1.96 * object$se
  ci.upper <- object$coef + 1.96 * object$se
  z <- object$coef/object$se
  p.value <- 2 * pnorm(-abs(z))
  TAB <- cbind(coef = object$coef, se = object$se, lower.95 = ci.lower, upper.95 = ci.upper, 
               z = z, p.value = p.value)
  if (dim(TAB)[1] == 1) {
    rownames(TAB) = as.character(object$fit.pha1$formula[[3]])  # retrieve the covariate name
  } else {
    rownames(TAB) = names(object$coef)
  }
  res <- list(call = object$call, coefficients = TAB)
  class(res) <- "summary.ah.ph2.only"
  res
}



#' @export
print.summary.ah.ph2.only <- function(x, digits = max(getOption("digits") - 4, 4), signif.stars = getOption("show.signif.stars"), 
                                      ...) {
  cat("Call:\n")
  print(x$call)
  cat("\n")
  printCoefmat(x$coefficients, digits = digits, signif.stars = signif.stars, P.values = TRUE, 
               has.Pvalue = TRUE, ...)
}


#' @export
summary.ah.2ph <- function(object, ...) {
  options(digits = 5)
  ci.lower <- object$coef - 1.96 * object$se
  ci.upper <- object$coef + 1.96 * object$se
  z <- object$coef/object$se
  p.value <- 2 * pnorm(-abs(z))
  TAB <- cbind(coef = object$coef, se = object$se, lower.95 = ci.lower, upper.95 = ci.upper, 
               z = z, p.value = p.value)
  if (dim(TAB)[1] == 1) {
    rownames(TAB) = as.character(object$fit.pha1$formula[[3]])  # retrieve the covariate name
  } else {
    rownames(TAB) = names(object$coef)
  }
  res <- list(call = object$call, coefficients = TAB)
  class(res) <- "summary.ah.2ph"
  res
}



#' @export
print.summary.ah.2ph <- function(x, digits = max(getOption("digits") - 4, 4), signif.stars = getOption("show.signif.stars"), 
                                 ...) {
  cat("Call:\n")
  print(x$call)
  cat("\n")
  printCoefmat(x$coefficients, digits = digits, signif.stars = signif.stars, P.values = TRUE, 
               has.Pvalue = TRUE, ...)
}