tbl_survfit: Creates table of survival probabilities

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

Creates table of survival probabilities

Description

\lifecycle

maturing Function takes a survfit object as an argument, and provides a formatted summary table of the results

Usage

tbl_survfit(x, ...)

## S3 method for class 'list'
tbl_survfit(
  x,
  times = NULL,
  probs = NULL,
  statistic = NULL,
  label = NULL,
  label_header = NULL,
  estimate_fun = NULL,
  missing = NULL,
  conf.level = 0.95,
  reverse = FALSE,
  quiet = NULL,
  ...
)

## S3 method for class 'survfit'
tbl_survfit(x, ...)

## S3 method for class 'data.frame'
tbl_survfit(x, y, include = everything(), ...)

Arguments

x	a survfit object, list of survfit objects, or a data frame. If a data frame is passed, a list of survfit objects is constructed using each variable as a stratifying variable.
...	For tbl_survfit.data.frame() and tbl_survfit.survfit() the arguments are passed to tbl_survfit.list(). They are not used when tbl_survfit.list() is called directly.
times	numeric vector of times for which to return survival probabilities.
probs	numeric vector of probabilities with values in (0,1) specifying the survival quantiles to return
statistic	string defining the statistics to present in the table. Default is "{estimate} ({conf.low}, {conf.high})"
label	List of formulas specifying variables labels, e.g. list(age ~ "Age, yrs", stage ~ "Path T Stage"), or a string for a single variable table.
label_header	string specifying column labels above statistics. Default is "{prob} Percentile" for survival percentiles, and "Time {time}" for n-year survival estimates
estimate_fun	function to format the Kaplan-Meier estimates. Default is style_percent() for survival probabilities and style_sigfig for survival times
missing	text to fill when estimate is not estimable. Default is "--"
conf.level	Confidence level for confidence intervals. Default is 0.95
reverse	Flip the probability reported, i.e. 1 - estimate. Default is FALSE. Does not apply to survival quantile requests
quiet	Logical indicating whether to print messages in console. Default is FALSE
y	outcome call, e.g. y = Surv(ttdeath, death)
include	Variable to include as stratifying variables.

Example Output

Example 1

Example 2

Example 3

Example 4

Author(s)

Daniel D. Sjoberg

See Also

Review list, formula, and selector syntax used throughout gtsummary

Other tbl_survfit tools: add_n.tbl_survfit(), add_nevent.tbl_survfit(), add_p.tbl_survfit(), modify, tbl_merge(), tbl_split(), tbl_stack(), tbl_strata()

Examples

library(survival)

# Example 1 ----------------------------------
# Pass single survfit() object
tbl_survfit_ex1 <- tbl_survfit(
  survfit(Surv(ttdeath, death) ~ trt, trial),
  times = c(12, 24),
  label_header = "**{time} Month**"
)

# Example 2 ----------------------------------
# Pass a data frame
tbl_survfit_ex2 <- tbl_survfit(
  trial,
  y = Surv(ttdeath, death),
  include = c(trt, grade),
  probs = 0.5,
  label_header = "**Median Survival**"
)

# Example 3 ----------------------------------
# Pass a list of survfit() objects
tbl_survfit_ex3 <-
  list(
    survfit(Surv(ttdeath, death) ~ 1, trial),
    survfit(Surv(ttdeath, death) ~ trt, trial)
  ) %>%
  tbl_survfit(times = c(12, 24))

# Example 4 Competing Events Example ---------
# adding a competing event for death (cancer vs other causes)
set.seed(1123)
library(dplyr, warn.conflicts = FALSE, quietly = TRUE)
trial2 <- trial %>%
  mutate(
    death_cr = case_when(
      death == 0 ~ "censor",
      runif(n()) < 0.5 ~ "death from cancer",
      TRUE ~ "death other causes"
    ) %>% factor()
  )

survfit_cr_ex4 <-
  survfit(Surv(ttdeath, death_cr) ~ grade, data = trial2) %>%
  tbl_survfit(times = c(12, 24), label = "Tumor Grade")

gtsummary documentation built on July 26, 2023, 5:27 p.m.