R/survival-cch.R

In tidyverse/broom: Convert Statistical Objects into Tidy Tibbles

#' @templateVar class cch
#' @template title_desc_tidy
#'
#' @param x An `cch` object returned from [survival::cch()].
#' @param conf.level confidence level for CI
#' @template param_unused_dots
#'
#' @evalRd return_tidy(regression = TRUE)
#'
#' @examplesIf rlang::is_installed(c("survival", "ggplot2"))
#'
#' # load libraries for models and data
#' library(survival)
#'
#' # examples come from cch documentation
#' subcoh <- nwtco$in.subcohort
#' selccoh <- with(nwtco, rel == 1 | subcoh == 1)
#' ccoh.data <- nwtco[selccoh, ]
#' ccoh.data$subcohort <- subcoh[selccoh]
#'
#' # central-lab histology
#' ccoh.data$histol <- factor(ccoh.data$histol, labels = c("FH", "UH"))
#'
#' # tumour stage
#' ccoh.data$stage <- factor(ccoh.data$stage, labels = c("I", "II", "III", "IV"))
#' ccoh.data$age <- ccoh.data$age / 12 # age in years
#'
#' # fit model
#' fit.ccP <- cch(Surv(edrel, rel) ~ stage + histol + age,
#'   data = ccoh.data,
#'   subcoh = ~subcohort, id = ~seqno, cohort.size = 4028
#' )
#'
#' # summarize model fit with tidiers + visualization
#' tidy(fit.ccP)
#'
#' # coefficient plot
#' library(ggplot2)
#'
#' ggplot(tidy(fit.ccP), aes(x = estimate, y = term)) +
#'   geom_point() +
#'   geom_errorbarh(aes(xmin = conf.low, xmax = conf.high), height = 0) +
#'   geom_vline(xintercept = 0)
#'
#' @aliases cch_tidiers
#' @export
#' @seealso [tidy()], [survival::cch()]
#' @family cch tidiers
#' @family survival tidiers
tidy.cch <- function(x, conf.level = .95, ...) {
  check_ellipses("exponentiate", "tidy", "cch", ...)

  s <- summary(x)
  co <- stats::coefficients(s)

  ret <- as_tidy_tibble(
    co,
    new_names = c("estimate", "std.error", "statistic", "p.value")
  )

  # add confidence interval
  ci <- unrowname(stats::confint(x, level = conf.level))
  colnames(ci) <- c("conf.low", "conf.high")
  as_tibble(cbind(ret, ci))
}


#' @templateVar class cch
#' @template title_desc_glance
#'
#' @inherit tidy.cch params examples
#'
#' @evalRd return_glance(
#'   "score",
#'   "rscore",
#'   "p.value",
#'   "iter",
#'   n = "number of predictions",
#'   nevent = "number of events"
#' )
#'
#' @export
#' @seealso [glance()], [survival::cch()]
#' @family cch tidiers
#' @family survival tidiers
glance.cch <- function(x, ...) {
  ret <- purrr::compact(unclass(x)[c(
    "score", "rscore", "wald.test", "iter",
    "n", "nevent"
  )])
  ret <- as_tibble(ret)
  rename(ret, p.value = wald.test)
}