R/import-standalone-survival.R

In topepo/yardstick: Tidy Characterizations of Model Performance

# Standalone file: do not edit by hand
# Source: <https://github.com/tidymodels/parsnip/blob/main/R/standalone-survival.R>
# ----------------------------------------------------------------------
#
# ---
# repo: tidymodels/parsnip
# file: standalone-survival.R
# last-updated: 2023-02-28
# license: https://unlicense.org
# ---

# This file provides a portable set of helper functions for Surv objects

# ## Changelog

# 2023-02-28:
# * Initial version


# @param surv A [survival::Surv()] object
# @details
# `.is_censored_right()` always returns a logical while
# `.check_censored_right()` will fail if `FALSE`.
#
# `.extract_status()` will return the data as 0/1 even if the original object
# used the legacy encoding of 1/2. See [survival::Surv()].
# @return
# - `.extract_surv_status()` returns a vector.
# - `.extract_surv_time()` returns a vector when the type is `"right"` or `"left"`
#    and a tibble otherwise.
# - Functions starting with `.is_` or `.check_` return logicals although the
#   latter will fail when `FALSE`.

# nocov start
# These are tested in the extratests repo since it would require a dependency
# on the survival package. https://github.com/tidymodels/extratests/pull/78
.is_censored_right <- function(surv) {
  .check_cens_type(surv, fail = FALSE)
}

.check_censored_right <- function(surv) {
  .check_cens_type(surv, fail = TRUE)
} # will add more as we need them

.extract_surv_time <- function(surv) {
  .is_surv(surv)
  keepers <- c("time", "start", "stop", "time1", "time2")
  res <- surv[, colnames(surv) %in% keepers]
  if (NCOL(res) > 1) {
    res <- dplyr::tibble(as.data.frame(res))
  }
  res
}

.extract_surv_status <- function(surv) {
  .is_surv(surv)
  res <- surv[, "status"]
  un_vals <- sort(unique(res))
  event_type_to_01 <- !(.extract_surv_type(surv) %in% c("interval", "interval2", "mstate"))
  if (
    event_type_to_01 &&
      (identical(un_vals, 1:2) || identical(un_vals, c(1.0, 2.0)))) {
    res <- res - 1
  }
  res
}

.is_surv <- function(surv, fail = TRUE) {
  is_surv <- inherits(surv, "Surv")
  if (!is_surv && fail) {
    abort("The object does not have class `Surv`.", call = NULL)
  }
  is_surv
}

.extract_surv_type <- function(surv) {
  attr(surv, "type")
}

.check_cens_type <- function(surv, type = "right", fail = TRUE) {
  .is_surv(surv)
  obj_type <- .extract_surv_type(surv)
  good_type <- all(obj_type %in% type)
  if (!good_type && fail) {
    c_list <- paste0("'", type, "'")
    msg <- cli::format_inline("For this usage, the allowed censoring type{?s} {?is/are}: {c_list}")
    abort(msg, call = NULL)
  }
  good_type
}

# nocov end