R/survival-coxph.R

In tidymodels/broom: Convert Statistical Objects into Tidy Tibbles

#' @templateVar class coxph
#' @template title_desc_tidy
#'
#' @param x A `coxph` object returned from [survival::coxph()].
#' @template param_confint
#' @template param_exponentiate
#' @param ... For `tidy()`, additional arguments passed to `summary(x, ...)`.
#' Otherwise ignored.
#'
#' @evalRd return_tidy(
#'   "estimate",
#'   "std.error",
#'   "statistic",
#'   "p.value"
#' )
#'
#' @examplesIf rlang::is_installed(c("survival", "ggplot2"))
#'
#' # load libraries for models and data
#' library(survival)
#'
#' # fit model
#' cfit <- coxph(Surv(time, status) ~ age + sex, lung)
#'
#' # summarize model fit with tidiers
#' tidy(cfit)
#' tidy(cfit, exponentiate = TRUE)
#'
#' lp <- augment(cfit, lung)
#' risks <- augment(cfit, lung, type.predict = "risk")
#' expected <- augment(cfit, lung, type.predict = "expected")
#'
#' glance(cfit)
#'
#' # also works on clogit models
#' resp <- levels(logan$occupation)
#' n <- nrow(logan)
#' indx <- rep(1:n, length(resp))
#' logan2 <- data.frame(
#'   logan[indx, ],
#'   id = indx,
#'   tocc = factor(rep(resp, each = n))
#' )
#'
#' logan2$case <- (logan2$occupation == logan2$tocc)
#'
#' cl <- clogit(case ~ tocc + tocc:education + strata(id), logan2)
#'
#' tidy(cl)
#' glance(cl)
#'
#' library(ggplot2)
#'
#' ggplot(lp, aes(age, .fitted, color = sex)) +
#'   geom_point()
#'
#' ggplot(risks, aes(age, .fitted, color = sex)) +
#'   geom_point()
#'
#' ggplot(expected, aes(time, .fitted, color = sex)) +
#'   geom_point()
#'
#' @aliases coxph_tidiers
#' @export
#' @seealso [tidy()], [survival::coxph()]
#' @family coxph tidiers
#' @family survival tidiers
tidy.coxph <- function(x, exponentiate = FALSE, conf.int = FALSE,
                       conf.level = .95, ...) {
  s <- summary(x, ...)
  co <- stats::coef(s)

  if (!is.null(x$frail)) {
    nn <- c("estimate", "std.error", "statistic", "p.value")
  } else if (isTRUE(s$used.robust)) {
    nn <- c("estimate", "std.error", "robust.se", "statistic", "p.value")
  } else {
    nn <- c("estimate", "std.error", "statistic", "p.value")
  }

  if (is.null(x$frail) && is.null(x$penalty)) {
    ret <- as_tidy_tibble(co[, -2, drop = FALSE], new_names = nn)
  } else {
    ret <- as_tidy_tibble(co[, -c(3, 5), drop = FALSE], new_names = nn)
  }

  if (conf.int) {
    ci <- broom_confint_terms(x, level = conf.level)
    ret <- dplyr::left_join(ret, ci, by = "term")
  }

  if (exponentiate) {
    ret <- exponentiate(ret)
  }

  as_tibble(ret)
}


#' @templateVar class coxph
#' @template title_desc_augment
#'
#' @inherit tidy.coxph params examples
#' @template param_data
#' @template param_newdata
#' @template param_type_residuals
#' @template param_type_predict
#' @template param_unused_dots
#'
#' @template augment_NAs
#'
#' @evalRd return_augment(".se.fit")
#'
#' @export
#' @seealso [augment()], [survival::coxph()]
#' @family coxph tidiers
#' @family survival tidiers
augment.coxph <- function(x, data = model.frame(x), newdata = NULL,
                          type.predict = "lp", type.residuals = "martingale",
                          ...) {
  augment_columns(x, data, newdata,
    type.predict = type.predict,
    type.residuals = type.residuals
  )
}

#' @templateVar class coxph
#' @template title_desc_glance
#'
#' @inherit tidy.coxph params examples
#'
#' @evalRd return_glance(
#'    "n",
#'    "nevent",
#'    "logLik",
#'    "AIC",
#'    "BIC",
#'    "nobs",
#'    .post = "See survival::coxph.object for additional column descriptions.")
#'
#' @export
#' @seealso [glance()], [survival::coxph()]
#' @family coxph tidiers
#' @family survival tidiers
glance.coxph <- function(x, ...) {
  s <- summary(x)
  # including all the test statistics and p-values as separate
  # columns. Admittedly not perfect but does capture most use cases.
  as_glance_tibble(
    n = s$n,
    nevent = s$nevent,
    statistic.log = s$logtest[1],
    p.value.log = s$logtest[3],
    statistic.sc = s$sctest[1],
    p.value.sc = s$sctest[3],
    statistic.wald = s$waldtest[1],
    p.value.wald = s$waldtest[3],
    statistic.robust = s$robscore[1],
    p.value.robust = s$robscore[3],
    r.squared = s$rsq[1],
    r.squared.max = s$rsq[2],
    concordance = s$concordance[1],
    std.error.concordance = s$concordance[2],
    logLik = as.numeric(stats::logLik(x)),
    AIC = stats::AIC(x),
    BIC = stats::BIC(x),
    nobs = stats::nobs(x),
    na_types = "iirrrrrrrrrrrrrrri"
  )
}