R/add_nevent.R

In gtsummary: Presentation-Ready Data Summary and Analytic Result Tables

#' Add number of events to a regression table
#'
#' Adds a column of the number of events to tables created with
#' [tbl_regression] or [tbl_uvregression].  Supported
#' model types are among GLMs with binomial distribution family (e.g.
#' [stats::glm], `lme4::glmer`, and
#' `geepack::geeglm`) and Cox
#' Proportion Hazards regression models ([survival::coxph]).
#'
#' @param x `tbl_regression` or `tbl_uvregression` object
#' @param ... Additional arguments passed to or from other methods.
#' @keywords internal
#' @export
#' @author Daniel D. Sjoberg
#' @seealso [add_nevent.tbl_regression], [add_nevent.tbl_uvregression],
#'  [add_nevent.tbl_survfit]

add_nevent <- function(x, ...) UseMethod("add_nevent")

#' Add event N to regression table
#'
#' @inheritParams add_n_regression
#' @name add_nevent_regression
#'
#' @examples
#' \donttest{
#' # Example 1 ----------------------------------
#' add_nevent.tbl_regression_ex1 <-
#'   trial %>%
#'   select(response, trt, grade) %>%
#'   tbl_uvregression(
#'     y = response,
#'     method = glm,
#'     method.args = list(family = binomial),
#'   ) %>%
#'   add_nevent()
#' # Example 2 ----------------------------------
#' add_nevent.tbl_regression_ex2 <-
#'   glm(response ~ age + grade, trial, family = binomial) %>%
#'   tbl_regression(exponentiate = TRUE) %>%
#'   add_nevent(location = "level")
#' }
#' @section Example Output:
#' \if{html}{Example 1}
#'
#' \if{html}{\out{
#' `r man_create_image_tag(file = "add_nevent.tbl_regression_ex1.png", width = "64")`
#' }}
#'
#' \if{html}{Example 2}
#'
#' \if{html}{\out{
#' `r man_create_image_tag(file = "add_nevent.tbl_regression_ex2.png", width = "64")`
#' }}
NULL

#' @rdname add_nevent_regression
#' @export
add_nevent.tbl_regression <- function(x, location = NULL, ...) {
  check_dots_empty(error = function(e) inform(c(e$message, e$body)))
  updated_call_list <- c(x$call_list, list(add_nevent = match.call()))
  location <- match.arg(location, choices = c("label", "level"), several.ok = TRUE)

  if ("level" %in% location && !"n_event" %in% x$table_styling$header$column) {
    abort("Reporting event N on level rows is not available for this model type.")
  }
  if ("label" %in% location && !"N_event" %in% x$table_styling$header$column) {
    abort("Reporting event N on label rows is not available for this model type.")
  }

  x$table_body$stat_nevent <- NA_integer_
  if ("N_event" %in% names(x$table_body)) {
    x$table_body$stat_nevent <- ifelse(x$table_body$row_type == "label",
      x$table_body$N_event %>% as.integer(),
      x$table_body$stat_nevent
    )
  }
  if ("n_event" %in% names(x$table_body)) {
    x$table_body$stat_nevent <- ifelse(x$table_body$row_type == "level",
      x$table_body$n_event %>% as.integer(),
      x$table_body$stat_nevent
    )
  }
  x <-
    x %>%
    modify_table_body(
      mutate,
      stat_nevent =
        case_when(
          !"level" %in% .env$location & .data$row_type %in% "level" ~ NA_integer_,
          !"label" %in% .env$location & .data$row_type %in% "label" &
            .data$var_type %in% c("categorical", "dichotomous") ~ NA_integer_,
          TRUE ~ .data$stat_nevent
        )
    ) %>%
    modify_table_body(
      dplyr::relocate,
      "stat_nevent",
      .before = "estimate"
    ) %>%
    modify_header(stat_nevent ~ "**Event N**")

  # fill in the Ns in the header table modify_stat_* columns
  x <- .fill_table_header_modify_stats(x)
  # add call list and return x
  x$call_list <- updated_call_list
  x
}

#' @export
#' @rdname add_nevent_regression
add_nevent.tbl_uvregression <- add_nevent.tbl_regression

#' Add column with number of observed events
#'
#' \lifecycle{maturing}
#' For each `survfit()` object summarized with `tbl_survfit()` this function
#' will add the total number of events observed in a new column.
#'
#' @param x object of class 'tbl_survfit'
#' @param ... Not used
#' @export
#' @family tbl_survfit tools
#' @examplesIf broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE)
#' \donttest{
#' library(survival)
#' fit1 <- survfit(Surv(ttdeath, death) ~ 1, trial)
#' fit2 <- survfit(Surv(ttdeath, death) ~ trt, trial)
#'
#' # Example 1 ----------------------------------
#' add_nevent.tbl_survfit_ex1 <-
#'   list(fit1, fit2) %>%
#'   tbl_survfit(times = c(12, 24)) %>%
#'   add_n() %>%
#'   add_nevent()
#' }
#' @section Example Output:
#' \if{html}{Example 1}
#'
#' \if{html}{\out{
#' `r man_create_image_tag(file = "add_nevent.tbl_survfit_ex1.png", width = "64")`
#' }}

add_nevent.tbl_survfit <- function(x, ...) {
  check_dots_empty(error = function(e) inform(c(e$message, e$body)))
  updated_call_list <- c(x$call_list, list(add_nevent = match.call()))

  # checking survfit is a standard (not multi-state)
  if (!purrr::every(x$meta_data$survfit, ~ rlang::is_empty(setdiff(class(.x), c("survfit", "survfit2"))))) {
    paste(
      "Each of the `survfit()` objects must have class 'survfit' only.",
      "Multi-state models are not supported by this function."
    ) %>%
      stringr::str_wrap() %>%
      stop(call. = FALSE)
  }

  # calculating event N --------------------------------------------------------
  x$table_body <-
    purrr::map2_dfr(
      x$meta_data$survfit, x$meta_data$variable,
      ~ tibble(
        nevent = broom::tidy(.x) %>% pull("n.event") %>% sum(),
        variable = .y,
        row_type = "label"
      )
    ) %>%
    {
      left_join(
        x$table_body, .,
        by = c("variable", "row_type")
      )
    } %>%
    select(any_of(c("variable", "row_type", "label", "N", "nevent")), everything())

  # adding N to table_styling and assigning header label -----------------------
  x <-
    modify_table_styling(
      x,
      columns = "nevent",
      label = "**Event N**",
      fmt_fun = style_number,
      hide = FALSE
    )

  # fill in the Ns in the header table modify_stat_* columns
  x <- .fill_table_header_modify_stats(x)
  # adding indicator to output that add_n was run on this data
  x$call_list <- updated_call_list
  x
}